data_EMD-62048
# 
_entry.id   EMD-62048 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.406 
_audit_conform.dict_location   http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 
# 
loop_
_database_2.database_id 
_database_2.database_code 
_database_2.pdbx_database_accession 
_database_2.pdbx_DOI 
PDB   9K46         pdb_00009k46 10.2210/pdb9k46/pdb 
WWPDB D_1300051577 ?            ?                   
EMDB  EMD-62048    ?            ?                   
# 
loop_
_pdbx_audit_revision_history.ordinal 
_pdbx_audit_revision_history.data_content_type 
_pdbx_audit_revision_history.major_revision 
_pdbx_audit_revision_history.minor_revision 
_pdbx_audit_revision_history.revision_date 
_pdbx_audit_revision_history.part_number 
1 'Structure model' 1 0 2025-11-12 ? 
2 'EM metadata'     1 0 2025-11-12 ? 
3 'Additional map'  1 0 2025-11-12 1 
4 FSC               1 0 2025-11-12 ? 
5 'Half map'        1 0 2025-11-12 1 
6 'Half map'        1 0 2025-11-12 2 
7 Image             1 0 2025-11-12 ? 
8 Mask              1 0 2025-11-12 1 
9 'Primary map'     1 0 2025-11-12 ? 
# 
loop_
_pdbx_audit_revision_details.ordinal 
_pdbx_audit_revision_details.revision_ordinal 
_pdbx_audit_revision_details.data_content_type 
_pdbx_audit_revision_details.provider 
_pdbx_audit_revision_details.type 
_pdbx_audit_revision_details.description 
_pdbx_audit_revision_details.details 
1 1 'Structure model' repository 'Initial release' ? ? 
2 2 'EM metadata'     repository 'Initial release' ? ? 
3 3 'Additional map'  repository 'Initial release' ? ? 
4 4 FSC               repository 'Initial release' ? ? 
5 5 'Half map'        repository 'Initial release' ? ? 
6 6 'Half map'        repository 'Initial release' ? ? 
7 7 Image             repository 'Initial release' ? ? 
8 8 Mask              repository 'Initial release' ? ? 
9 9 'Primary map'     repository 'Initial release' ? ? 
# 
loop_
_pdbx_database_related.db_name 
_pdbx_database_related.details 
_pdbx_database_related.db_id 
_pdbx_database_related.content_type 
EMDB 'Cryo-EM structure of Arabidopsis thaliana H2A.W-H3.3-nucleosome  with Arabidopsis native 147bp DNA 15.2-2 (C2 symmetry)' 
EMD-62048 'associated EM volume' 
EMDB .                                                                                                                         
EMD-62047 'other EM volume'      
# 
_citation.abstract                  ? 
_citation.abstract_id_CAS           ? 
_citation.book_id_ISBN              ? 
_citation.book_publisher            ? 
_citation.book_publisher_city       ? 
_citation.book_title                ? 
_citation.coordinate_linkage        ? 
_citation.country                   ? 
_citation.database_id_Medline       ? 
_citation.details                   ? 
_citation.id                        primary 
_citation.journal_abbrev            'To Be Published' 
_citation.journal_id_ASTM           ? 
_citation.journal_id_CSD            0353 
_citation.journal_id_ISSN           ? 
_citation.journal_full              ? 
_citation.journal_issue             ? 
_citation.journal_volume            ? 
_citation.language                  ? 
_citation.page_first                ? 
_citation.page_last                 ? 
_citation.title                     'Functional redundancy of core histone H2A and its variants in Arabidopsis' 
_citation.year                      ? 
_citation.database_id_CSD           ? 
_citation.pdbx_database_id_DOI      ? 
_citation.pdbx_database_id_PubMed   ? 
_citation.pdbx_database_id_patent   ? 
_citation.unpublished_flag          ? 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Wang, Y.' 1 0000-0001-6786-9032 
primary 'Dong, A.' 2 0000-0002-2075-4235 
# 
loop_
_entity.id 
_entity.type 
_entity.src_method 
_entity.pdbx_description 
_entity.formula_weight 
_entity.pdbx_number_of_molecules 
_entity.pdbx_ec 
_entity.pdbx_mutation 
_entity.pdbx_fragment 
_entity.details 
1 polymer man 'Histone H3.3'           15440.144 2 ? ? ? ? 
2 polymer man 'Histone H4'             11436.467 2 ? ? ? ? 
3 polymer man 'Probable histone H2A.7' 15997.942 2 ? ? ? ? 
4 polymer man 'Histone H2B.1'          16439.291 2 ? ? ? ? 
5 polymer syn '15.2.2 DNA (147-MER)'   45071.871 1 ? ? ? ? 
6 polymer syn '15.2.2 DNA (147-MER)'   45654.219 1 ? ? ? ? 
# 
loop_
_entity_poly.entity_id 
_entity_poly.type 
_entity_poly.pdbx_seq_one_letter_code 
1 'polypeptide(L)'        
;MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK
TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
;
2 'polypeptide(L)'        
;MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK
TVTAMDVVYALKRQGRTLYGFGG
;
3 'polypeptide(L)'        
;MESTGKVKKAFGGRKPPGAPKTKSVSKSMKAGLQFPVGRITRFLKKGRYAQRLGGGAPVYMAAVLEYLAAEVLELAGNAA
RDNKKSRIIPRHLLLAIRNDEELGKLLSGVTIAHGGVLPNINSVLLPKKSATKPAEEKATKSPVKSPKKA
;
4 'polypeptide(L)'        
;MAPRAEKKPAEKKTAAERPVEENKAAEKAPAEKKPKAGKKLPPKEAGDKKKKRSKKNVETYKIYIFKVLKQVHPDIGISS
KAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
;
5 polydeoxyribonucleotide 
;(DA)(DC)(DC)(DT)(DT)(DT)(DA)(DT)(DT)(DG)(DA)(DC)(DT)(DC)(DC)(DA)(DT)(DA)(DA)(DT)
(DT)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DT)(DC)(DG)(DA)
(DT)(DT)(DC)(DA)(DA)(DC)(DT)(DG)(DT)(DC)(DA)(DA)(DT)(DA)(DA)(DC)(DT)(DT)(DC)(DA)
(DA)(DA)(DT)(DG)(DA)(DA)(DG)(DC)(DA)(DA)(DG)(DA)(DG)(DC)(DC)(DT)(DT)(DA)(DT)(DC)
(DG)(DT)(DA)(DT)(DT)(DC)(DT)(DC)(DC)(DG)(DC)(DA)(DC)(DG)(DA)(DT)(DG)(DG)(DT)(DG)
(DC)(DT)(DT)(DT)(DA)(DA)(DT)(DC)(DC)(DA)(DC)(DC)(DG)(DC)(DA)(DA)(DC)(DT)(DT)(DT)
(DC)(DC)(DT)(DC)(DT)(DT)(DT)(DA)(DA)(DT)(DA)(DA)(DA)(DG)(DG)(DC)(DA)(DC)(DA)(DA)
(DG)(DC)(DA)(DT)(DT)(DA)(DA)
;
6 polydeoxyribonucleotide 
;(DT)(DT)(DA)(DA)(DT)(DG)(DC)(DT)(DT)(DG)(DT)(DG)(DC)(DC)(DT)(DT)(DT)(DA)(DT)(DT)
(DA)(DA)(DA)(DG)(DA)(DG)(DG)(DA)(DA)(DA)(DG)(DT)(DT)(DG)(DC)(DG)(DG)(DT)(DG)(DG)
(DA)(DT)(DT)(DA)(DA)(DA)(DG)(DC)(DA)(DC)(DC)(DA)(DT)(DC)(DG)(DT)(DG)(DC)(DG)(DG)
(DA)(DG)(DA)(DA)(DT)(DA)(DC)(DG)(DA)(DT)(DA)(DA)(DG)(DG)(DC)(DT)(DC)(DT)(DT)(DG)
(DC)(DT)(DT)(DC)(DA)(DT)(DT)(DT)(DG)(DA)(DA)(DG)(DT)(DT)(DA)(DT)(DT)(DG)(DA)(DC)
(DA)(DG)(DT)(DT)(DG)(DA)(DA)(DT)(DC)(DG)(DA)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)
(DT)(DT)(DG)(DG)(DT)(DC)(DA)(DA)(DT)(DT)(DA)(DT)(DG)(DG)(DA)(DG)(DT)(DC)(DA)(DA)
(DT)(DA)(DA)(DA)(DG)(DG)(DT)
;
# 
loop_
_entity_src_gen.entity_id 
_entity_src_gen.pdbx_src_id 
_entity_src_gen.pdbx_alt_source_flag 
_entity_src_gen.pdbx_seq_type 
_entity_src_gen.pdbx_beg_seq_num 
_entity_src_gen.pdbx_end_seq_num 
_entity_src_gen.gene_src_common_name 
_entity_src_gen.gene_src_genus 
_entity_src_gen.pdbx_gene_src_gene 
_entity_src_gen.gene_src_species 
_entity_src_gen.gene_src_strain 
_entity_src_gen.gene_src_tissue 
_entity_src_gen.gene_src_tissue_fraction 
_entity_src_gen.gene_src_details 
_entity_src_gen.pdbx_gene_src_fragment 
_entity_src_gen.pdbx_gene_src_scientific_name 
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 
_entity_src_gen.pdbx_gene_src_variant 
_entity_src_gen.pdbx_gene_src_cell_line 
_entity_src_gen.pdbx_gene_src_atcc 
_entity_src_gen.pdbx_gene_src_culture_collection 
_entity_src_gen.pdbx_gene_src_organ 
_entity_src_gen.pdbx_gene_src_organelle 
_entity_src_gen.pdbx_gene_src_cell 
_entity_src_gen.pdbx_gene_src_cellular_location 
_entity_src_gen.host_org_common_name 
_entity_src_gen.pdbx_host_org_scientific_name 
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 
_entity_src_gen.host_org_genus 
_entity_src_gen.pdbx_host_org_gene 
_entity_src_gen.pdbx_host_org_organ 
_entity_src_gen.host_org_species 
_entity_src_gen.pdbx_host_org_tissue 
_entity_src_gen.pdbx_host_org_tissue_fraction 
_entity_src_gen.pdbx_host_org_strain 
_entity_src_gen.pdbx_host_org_variant 
_entity_src_gen.pdbx_host_org_cell_line 
_entity_src_gen.pdbx_host_org_atcc 
_entity_src_gen.pdbx_host_org_culture_collection 
_entity_src_gen.pdbx_host_org_cell 
_entity_src_gen.pdbx_host_org_organelle 
_entity_src_gen.pdbx_host_org_cellular_location 
_entity_src_gen.pdbx_host_org_vector_type 
_entity_src_gen.pdbx_host_org_vector 
_entity_src_gen.host_org_details 
_entity_src_gen.expression_system_id 
_entity_src_gen.plasmid_name 
_entity_src_gen.plasmid_details 
_entity_src_gen.pdbx_description 
1 1 sample 'Biological sequence' 1 136 'thale cress' ? 
'HTR4, At4g40030, T5J17.200, HTR5, At4g40040, T5J17.210, HTR8, At5g10980, T30N20_250, T5K6.6' ? ? ? ? ? ? 'Arabidopsis thaliana' 
3702 ? ? ? ? ? ? ? ? ? 'Escherichia coli' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
2 1 sample 'Biological sequence' 1 103 'thale cress' ? 
;At1g07660, F24B9.25, At1g07820, F24B9.8, At2g28740, F8N16.2, T11P11.4, At3g45930, F16L2_140, At3g46320, F18L15.40, At3g53730, F5K20_30, At5g59690, MTH12.10, At5g59970, MMN10.22
;
? ? ? ? ? ? 'Arabidopsis thaliana' 3702 ? ? ? ? ? ? ? ? ? 'Escherichia coli' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
3 1 sample 'Biological sequence' 1 150 'thale cress' ? 'At5g59870, MMN10.22, MMN10_90' ? ? ? ? ? ? 'Arabidopsis thaliana' 3702 ? ? 
? ? ? ? ? ? ? 'Escherichia coli' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
4 1 sample 'Biological sequence' 1 148 'thale cress' ? 'At1g07790, F24B9.10' ? ? ? ? ? ? 'Arabidopsis thaliana' 3702 ? ? ? ? ? ? ? 
? ? 'Escherichia coli' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
# 
loop_
_pdbx_entity_src_syn.entity_id 
_pdbx_entity_src_syn.pdbx_src_id 
_pdbx_entity_src_syn.pdbx_alt_source_flag 
_pdbx_entity_src_syn.pdbx_beg_seq_num 
_pdbx_entity_src_syn.pdbx_end_seq_num 
_pdbx_entity_src_syn.organism_scientific 
_pdbx_entity_src_syn.organism_common_name 
_pdbx_entity_src_syn.ncbi_taxonomy_id 
_pdbx_entity_src_syn.details 
5 1 sample 1 147 'Arabidopsis thaliana' 'thale cress' 3702 ? 
6 1 sample 1 147 'Arabidopsis thaliana' 'thale cress' 3702 ? 
# 
loop_
_chem_comp.id 
_chem_comp.type 
_chem_comp.mon_nstd_flag 
_chem_comp.name 
_chem_comp.pdbx_synonyms 
_chem_comp.formula 
_chem_comp.formula_weight 
ALA 'L-peptide linking' y ALANINE                              ? 'C3 H7 N O2'      89.093  
ARG 'L-peptide linking' y ARGININE                             ? 'C6 H15 N4 O2 1'  175.209 
ASN 'L-peptide linking' y ASPARAGINE                           ? 'C4 H8 N2 O3'     132.118 
ASP 'L-peptide linking' y 'ASPARTIC ACID'                      ? 'C4 H7 N O4'      133.103 
CYS 'L-peptide linking' y CYSTEINE                             ? 'C3 H7 N O2 S'    121.158 
DA  'DNA linking'       y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 
DC  'DNA linking'       y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE"  ? 'C9 H14 N3 O7 P'  307.197 
DG  'DNA linking'       y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 
DT  'DNA linking'       y "THYMIDINE-5'-MONOPHOSPHATE"         ? 'C10 H15 N2 O8 P' 322.208 
GLN 'L-peptide linking' y GLUTAMINE                            ? 'C5 H10 N2 O3'    146.144 
GLU 'L-peptide linking' y 'GLUTAMIC ACID'                      ? 'C5 H9 N O4'      147.129 
GLY 'peptide linking'   y GLYCINE                              ? 'C2 H5 N O2'      75.067  
HIS 'L-peptide linking' y HISTIDINE                            ? 'C6 H10 N3 O2 1'  156.162 
ILE 'L-peptide linking' y ISOLEUCINE                           ? 'C6 H13 N O2'     131.173 
LEU 'L-peptide linking' y LEUCINE                              ? 'C6 H13 N O2'     131.173 
LYS 'L-peptide linking' y LYSINE                               ? 'C6 H15 N2 O2 1'  147.195 
MET 'L-peptide linking' y METHIONINE                           ? 'C5 H11 N O2 S'   149.211 
PHE 'L-peptide linking' y PHENYLALANINE                        ? 'C9 H11 N O2'     165.189 
PRO 'L-peptide linking' y PROLINE                              ? 'C5 H9 N O2'      115.130 
SER 'L-peptide linking' y SERINE                               ? 'C3 H7 N O3'      105.093 
THR 'L-peptide linking' y THREONINE                            ? 'C4 H9 N O3'      119.119 
TYR 'L-peptide linking' y TYROSINE                             ? 'C9 H11 N O3'     181.189 
VAL 'L-peptide linking' y VALINE                               ? 'C5 H11 N O2'     117.146 
# 
_exptl.entry_id         EMD-62048 
_exptl.details          ? 
_exptl.method           'ELECTRON MICROSCOPY' 
_exptl.method_details   ? 
# 
_struct_keywords.entry_id        EMD-62048 
_struct_keywords.text            'nucleosome, histone, H2A.W, H3.3, Arabidopsis, NUCLEAR PROTEIN/DNA, NUCLEAR PROTEIN-DNA complex' 
_struct_keywords.pdbx_keywords   'NUCLEAR PROTEIN/DNA' 
_struct_keywords.pdbx_details    ? 
# 
loop_
_struct_ref.id 
_struct_ref.db_name 
_struct_ref.db_code 
_struct_ref.entity_id 
1 UNP H33_ARATH  1 
2 UNP H4_ARATH   2 
3 UNP H2A7_ARATH 3 
4 UNP H2B1_ARATH 4 
5 GB  AL161580.2 5 
6 GB  AL161580.2 6 
# 
_em_3d_fitting.id                1 
_em_3d_fitting.entry_id          EMD-62048 
_em_3d_fitting.method            ? 
_em_3d_fitting.target_criteria   ? 
_em_3d_fitting.details           ? 
_em_3d_fitting.overall_b_value   ? 
_em_3d_fitting.ref_space         ? 
_em_3d_fitting.ref_protocol      ? 
# 
_em_3d_reconstruction.entry_id                    EMD-62048 
_em_3d_reconstruction.id                          1 
_em_3d_reconstruction.method                      ? 
_em_3d_reconstruction.algorithm                   ? 
_em_3d_reconstruction.citation_id                 ? 
_em_3d_reconstruction.details                     ? 
_em_3d_reconstruction.resolution                  2.85 
_em_3d_reconstruction.resolution_method           'FSC 0.143 CUT-OFF' 
_em_3d_reconstruction.magnification_calibration   ? 
_em_3d_reconstruction.nominal_pixel_size          ? 
_em_3d_reconstruction.actual_pixel_size           ? 
_em_3d_reconstruction.num_particles               165777 
_em_3d_reconstruction.euler_angles_details        ? 
_em_3d_reconstruction.num_class_averages          ? 
_em_3d_reconstruction.fsc_type                    'EVEN/ODD MAPS REFINED TOTALLY INDEPENDENT (GOLD STANDARD)' 
_em_3d_reconstruction.refinement_type             ? 
_em_3d_reconstruction.image_processing_id         1 
_em_3d_reconstruction.symmetry_type               POINT 
# 
_em_buffer.id            1 
_em_buffer.specimen_id   1 
_em_buffer.name          ? 
_em_buffer.details       ? 
_em_buffer.pH            7.4 
# 
_em_entity_assembly.id                   1 
_em_entity_assembly.parent_id            0 
_em_entity_assembly.source               RECOMBINANT 
_em_entity_assembly.type                 COMPLEX 
_em_entity_assembly.name                 'Arabidopsis thaliana H2A.W-H3.3-nucleosome  with Arabidopsis native 147bp DNA 15.2.2' 
_em_entity_assembly.details              ? 
_em_entity_assembly.go_id                ? 
_em_entity_assembly.ipr_id               ? 
_em_entity_assembly.synonym              ? 
_em_entity_assembly.number_of_copies     ? 
_em_entity_assembly.oligomeric_details   ? 
_em_entity_assembly.entity_id_list       '1, 2, 3, 4, 5, 6' 
_em_entity_assembly.mutant_flag          ? 
_em_entity_assembly.chimera              NO 
# 
_em_imaging.entry_id                        EMD-62048 
_em_imaging.id                              1 
_em_imaging.astigmatism                     ? 
_em_imaging.electron_beam_tilt_params       ? 
_em_imaging.residual_tilt                   ? 
_em_imaging.sample_support_id               1 
_em_imaging.detector_id                     1 
_em_imaging.scans_id                        1 
_em_imaging.microscope_id                   ? 
_em_imaging.microscope_model                'TFS KRIOS' 
_em_imaging.specimen_holder_type            ? 
_em_imaging.specimen_holder_model           'FEI TITAN KRIOS AUTOGRID HOLDER' 
_em_imaging.details                         ? 
_em_imaging.date                            ? 
_em_imaging.accelerating_voltage            300 
_em_imaging.illumination_mode               'FLOOD BEAM' 
_em_imaging.mode                            'BRIGHT FIELD' 
_em_imaging.nominal_cs                      ? 
_em_imaging.nominal_defocus_min             900 
_em_imaging.nominal_defocus_max             1800 
_em_imaging.calibrated_defocus_min          ? 
_em_imaging.calibrated_defocus_max          ? 
_em_imaging.tilt_angle_min                  ? 
_em_imaging.tilt_angle_max                  ? 
_em_imaging.nominal_magnification           ? 
_em_imaging.calibrated_magnification        ? 
_em_imaging.electron_source                 'FIELD EMISSION GUN' 
_em_imaging.citation_id                     ? 
_em_imaging.temperature                     ? 
_em_imaging.detector_distance               ? 
_em_imaging.recording_temperature_minimum   ? 
_em_imaging.recording_temperature_maximum   ? 
_em_imaging.alignment_procedure             'COMA FREE' 
_em_imaging.c2_aperture_diameter            ? 
_em_imaging.specimen_id                     1 
_em_imaging.cryogen                         NITROGEN 
_em_imaging.objective_aperture              ? 
_em_imaging.microscope_serial_number        ? 
_em_imaging.microscope_version              ? 
# 
_em_vitrification.entry_id                EMD-62048 
_em_vitrification.id                      1 
_em_vitrification.sample_preparation_id   ? 
_em_vitrification.specimen_id             1 
_em_vitrification.cryogen_name            ETHANE 
_em_vitrification.humidity                ? 
_em_vitrification.temp                    ? 
_em_vitrification.chamber_temperature     ? 
_em_vitrification.instrument              ? 
_em_vitrification.method                  ? 
_em_vitrification.time_resolved_state     ? 
_em_vitrification.citation_id             ? 
_em_vitrification.details                 ? 
# 
_em_experiment.entry_id                EMD-62048 
_em_experiment.id                      1 
_em_experiment.reconstruction_method   'SINGLE PARTICLE' 
_em_experiment.aggregation_state       PARTICLE 
_em_experiment.entity_assembly_id      1 
# 
_em_single_particle_entity.entry_id              EMD-62048 
_em_single_particle_entity.id                    1 
_em_single_particle_entity.image_processing_id   1 
_em_single_particle_entity.point_symmetry        C2 
# 
_em_admin.current_status        REL 
_em_admin.deposition_date       2024-10-21 
_em_admin.deposition_site       PDBJ 
_em_admin.details               ? 
_em_admin.entry_id              EMD-62048 
_em_admin.last_update           2025-11-12 
_em_admin.map_release_date      2025-11-12 
_em_admin.header_release_date   2025-11-12 
_em_admin.obsoleted_date        ? 
_em_admin.title                 
'Cryo-EM structure of Arabidopsis thaliana H2A.W-H3.3-nucleosome  with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry)' 
_em_admin.process_site          PDBC 
_em_admin.composite_map         NO 
# 
loop_
_em_author_list.author 
_em_author_list.identifier_ORCID 
_em_author_list.ordinal 
'Wang, Y.' 0000-0001-6786-9032 1 
'Dong, A.' 0000-0002-2075-4235 2 
# 
_em_ctf_correction.amplitude_correction              ? 
_em_ctf_correction.amplitude_correction_factor       ? 
_em_ctf_correction.amplitude_correction_space        ? 
_em_ctf_correction.correction_operation              ? 
_em_ctf_correction.details                           ? 
_em_ctf_correction.em_image_processing_id            1 
_em_ctf_correction.id                                1 
_em_ctf_correction.phase_reversal                    ? 
_em_ctf_correction.phase_reversal_anisotropic        ? 
_em_ctf_correction.phase_reversal_correction_space   ? 
_em_ctf_correction.type                              NONE 
# 
_em_db_reference.access_code    9K46 
_em_db_reference.db_name        PDB 
_em_db_reference.details        ? 
_em_db_reference.id             1 
_em_db_reference.relationship   'IN FRAME' 
# 
_em_entity_assembly_naturalsource.cell                 ? 
_em_entity_assembly_naturalsource.cellular_location    ? 
_em_entity_assembly_naturalsource.entity_assembly_id   1 
_em_entity_assembly_naturalsource.id                   2 
_em_entity_assembly_naturalsource.ncbi_tax_id          3702 
_em_entity_assembly_naturalsource.organism             'Arabidopsis thaliana' 
_em_entity_assembly_naturalsource.organelle            ? 
_em_entity_assembly_naturalsource.organ                ? 
_em_entity_assembly_naturalsource.strain               ? 
_em_entity_assembly_naturalsource.tissue               ? 
_em_entity_assembly_naturalsource.details              ? 
# 
_em_entity_assembly_recombinant.cell                 ? 
_em_entity_assembly_recombinant.entity_assembly_id   1 
_em_entity_assembly_recombinant.id                   2 
_em_entity_assembly_recombinant.ncbi_tax_id          562 
_em_entity_assembly_recombinant.organism             'Escherichia coli' 
_em_entity_assembly_recombinant.plasmid              ? 
_em_entity_assembly_recombinant.strain               ? 
# 
loop_
_em_euler_angle_assignment.details 
_em_euler_angle_assignment.id 
_em_euler_angle_assignment.image_processing_id 
_em_euler_angle_assignment.order 
_em_euler_angle_assignment.proj_matching_angular_sampling 
_em_euler_angle_assignment.proj_matching_merit_function 
_em_euler_angle_assignment.proj_matching_num_projections 
_em_euler_angle_assignment.type 
? 1 1 INITIAL ? ? ? 'MAXIMUM LIKELIHOOD' 
? 2 1 FINAL   ? ? ? 'MAXIMUM LIKELIHOOD' 
# 
_em_image_processing.details              ? 
_em_image_processing.id                   1 
_em_image_processing.image_recording_id   1 
# 
_em_image_recording.average_exposure_time               ? 
_em_image_recording.avg_electron_dose_per_subtomogram   ? 
_em_image_recording.avg_electron_dose_per_image         50 
_em_image_recording.details                             ? 
_em_image_recording.detector_mode                       ? 
_em_image_recording.film_or_detector_model              'GATAN K3 (6k x 4k)' 
_em_image_recording.id                                  1 
_em_image_recording.imaging_id                          1 
_em_image_recording.num_diffraction_images              ? 
_em_image_recording.num_grids_imaged                    ? 
_em_image_recording.num_real_images                     ? 
# 
loop_
_em_map.annotation_details 
_em_map.axis_order_fast 
_em_map.axis_order_medium 
_em_map.axis_order_slow 
_em_map.cell_a 
_em_map.cell_b 
_em_map.cell_c 
_em_map.cell_alpha 
_em_map.cell_beta 
_em_map.cell_gamma 
_em_map.contour_level 
_em_map.contour_level_source 
_em_map.data_type 
_em_map.dimensions_col 
_em_map.dimensions_row 
_em_map.dimensions_sec 
_em_map.endian_type 
_em_map.file 
_em_map.format 
_em_map.id 
_em_map.partition 
_em_map.entry_id 
_em_map.label 
_em_map.limit_col 
_em_map.limit_row 
_em_map.limit_sec 
_em_map.origin_col 
_em_map.origin_row 
_em_map.origin_sec 
_em_map.pixel_spacing_x 
_em_map.pixel_spacing_y 
_em_map.pixel_spacing_z 
_em_map.size_kb 
_em_map.spacing_x 
_em_map.spacing_y 
_em_map.spacing_z 
_em_map.statistics_average 
_em_map.statistics_maximum 
_em_map.statistics_minimum 
_em_map.statistics_std 
_em_map.symmetry_space_group 
_em_map.type 
map         X Y Z 274.432 274.432 274.432 90.0 90.0 90.0 0.2  author 'Image stored as floating point number (4 bytes)' 256 256 256 
big emd_62048.map.gz              CCP4 1 1 EMD-62048 ::::EMDATABANK.org::::EMD-62048:::: 255 255 255 0 0 0 1.072 1.072 1.072 
67109888 256 256 256 -0.0039506764 1.3995342 -0.46859258 0.05079715  1 'primary map'    
map_half_B  X Y Z 274.432 274.432 274.432 90.0 90.0 90.0 0.55 author 'Image stored as floating point number (4 bytes)' 256 256 256 
big emd_62048_half_map_2.map.gz   CCP4 2 2 EMD-62048 ::::EMDATABANK.org::::EMD-62048:::: 255 255 255 0 0 0 1.072 1.072 1.072 
67109888 256 256 256 7.857353E-4   1.5192089 -0.51059973 0.07413724  1 'half map'       
map_half_A  X Y Z 274.432 274.432 274.432 90.0 90.0 90.0 0.55 author 'Image stored as floating point number (4 bytes)' 256 256 256 
big emd_62048_half_map_1.map.gz   CCP4 3 1 EMD-62048 ::::EMDATABANK.org::::EMD-62048:::: 255 255 255 0 0 0 1.072 1.072 1.072 
67109888 256 256 256 7.892219E-4   1.5251856 -0.4662553  0.074136905 1 'half map'       
mask_refine X Y Z 274.432 274.432 274.432 90.0 90.0 90.0 0.9  author 'Image stored as floating point number (4 bytes)' 256 256 256 
big emd_62048_msk_1.map           CCP4 4 1 EMD-62048 ::::EMDATABANK.org::::EMD-62048:::: 255 255 255 0 0 0 1.072 1.072 1.072 
67109888 256 256 256 0.036401678   1.0       0.0         0.18039292  1 mask             
map_sharp   X Y Z 274.432 274.432 274.432 90.0 90.0 90.0 0.55 author 'Image stored as floating point number (4 bytes)' 256 256 256 
big emd_62048_additional_1.map.gz CCP4 5 1 EMD-62048 ::::EMDATABANK.org::::EMD-62048:::: 255 255 255 0 0 0 1.072 1.072 1.072 
67109888 256 256 256 -0.0018501938 4.209612  -2.1516314  0.1077977   1 'additional map' 
# 
loop_
_em_software.category 
_em_software.details 
_em_software.id 
_em_software.image_processing_id 
_em_software.fitting_id 
_em_software.imaging_id 
_em_software.name 
_em_software.version 
_em_software.reference_DOI 
'PARTICLE SELECTION'            ? 1  1 ? ? ?         ?            ? 
'MODEL REFINEMENT'              ? 2  ? ? ? PHENIX    1.20.1_4487: ? 
'IMAGE ACQUISITION'             ? 3  1 ? 1 EPU       ?            ? 
MASKING                         ? 4  1 1 1 ?         ?            ? 
'CTF CORRECTION'                ? 5  1 ? ? ?         ?            ? 
'LAYERLINE INDEXING'            ? 6  1 1 1 ?         ?            ? 
'DIFFRACTION INDEXING'          ? 7  1 1 1 ?         ?            ? 
'MODEL FITTING'                 ? 8  1 1 1 ?         ?            ? 
OTHER                           ? 9  1 1 1 ?         ?            ? 
'INITIAL EULER ASSIGNMENT'      ? 10 1 ? ? ?         ?            ? 
'FINAL EULER ASSIGNMENT'        ? 11 1 ? ? ?         ?            ? 
CLASSIFICATION                  ? 12 1 ? ? ?         ?            ? 
RECONSTRUCTION                  ? 13 1 ? ? cryoSPARC 4.3          ? 
'VOLUME SELECTION'              ? 14 1 1 1 ?         ?            ? 
'SERIES ALIGNMENT'              ? 15 1 1 1 ?         ?            ? 
'MOLECULAR REPLACEMENT'         ? 16 1 1 1 ?         ?            ? 
'LATTICE DISTORTION CORRECTION' ? 17 1 1 1 ?         ?            ? 
'SYMMETRY DETERMINATION'        ? 18 1 1 1 ?         ?            ? 
'CRYSTALLOGRAPHY MERGING'       ? 19 1 1 1 ?         ?            ? 
# 
_em_specimen.concentration           1 
_em_specimen.details                 ? 
_em_specimen.embedding_applied       NO 
_em_specimen.experiment_id           1 
_em_specimen.id                      1 
_em_specimen.shadowing_applied       NO 
_em_specimen.staining_applied        NO 
_em_specimen.vitrification_applied   YES 
# 
_em_start_model.details                          ? 
_em_start_model.emdb_id                          ? 
_em_start_model.id                               1 
_em_start_model.image_processing_id              1 
_em_start_model.insilico_model                   ? 
_em_start_model.orthogonal_tilt_angle1           ? 
_em_start_model.orthogonal_tilt_angle2           ? 
_em_start_model.orthogonal_tilt_num_images       ? 
_em_start_model.other                            ? 
_em_start_model.pdb_id                           ? 
_em_start_model.random_conical_tilt_angle        ? 
_em_start_model.random_conical_tilt_num_images   ? 
_em_start_model.type                             NONE 
# 
_pdbx_audit_support.funding_organization   'National Natural Science Foundation of China (NSFC)' 
_pdbx_audit_support.country                China 
_pdbx_audit_support.grant_number           31930017 
_pdbx_audit_support.details                ? 
_pdbx_audit_support.ordinal                1 
# 
