data_EMD-46713
# 
_entry.id   EMD-46713 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.409 
_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 
WWPDB D_1000287779 ? ? 
EMDB  EMD-46713    ? ? 
# 
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 'EM metadata' 1 0 2025-12-17 ? 
2 'Half map'    1 0 2025-12-17 1 
3 'Half map'    1 0 2025-12-17 2 
4 Image         1 0 2025-12-17 ? 
5 'Primary map' 1 0 2025-12-17 ? 
# 
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 'EM metadata' repository 'Initial release' ? ? 
2 2 'Half map'    repository 'Initial release' ? ? 
3 3 'Half map'    repository 'Initial release' ? ? 
4 4 Image         repository 'Initial release' ? ? 
5 5 'Primary map' repository 'Initial release' ? ? 
# 
_pdbx_database_related.db_name        EMDB 
_pdbx_database_related.details        . 
_pdbx_database_related.db_id          EMD-46713 
_pdbx_database_related.content_type   'associated 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                   US 
_citation.database_id_Medline       ? 
_citation.details                   ? 
_citation.id                        primary 
_citation.journal_abbrev            'Sci Adv' 
_citation.journal_id_ASTM           ? 
_citation.journal_id_CSD            ? 
_citation.journal_id_ISSN           2375-2548 
_citation.journal_full              ? 
_citation.journal_issue             ? 
_citation.journal_volume            11 
_citation.language                  ? 
_citation.page_first                eady9156 
_citation.page_last                 eady9156 
_citation.title                     
'How ATP and dATP reposition class III ribonucleotide reductase cone domains to regulate enzyme activity.' 
_citation.year                      2025 
_citation.database_id_CSD           ? 
_citation.pdbx_database_id_DOI      10.1126/sciadv.ady9156 
_citation.pdbx_database_id_PubMed   41313771 
_citation.pdbx_database_id_patent   ? 
_citation.unpublished_flag          ? 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Andree, G.A.'       1 0000-0002-5620-6951 
primary 'Miller-Brown, K.R.' 2 0000-0003-1963-2908 
primary 'Zhao, Z.'           3 0000-0002-5368-4130 
primary 'Smith, A.K.'        4 0000-0003-4539-1714 
primary 'Dawson, C.D.'       5 ?                   
primary 'Deredge, D.J.'      6 0000-0002-6897-6523 
primary 'Drennan, C.L.'      7 0000-0001-5486-2755 
# 
_exptl.entry_id         EMD-46713 
_exptl.details          ? 
_exptl.method           'ELECTRON MICROSCOPY' 
_exptl.method_details   ? 
# 
_struct_keywords.entry_id        EMD-46713 
_struct_keywords.text            
'Ribonucleotide reductase, allosteric regulation, cone domain, glycyl radical enzyme, OXIDOREDUCTASE' 
_struct_keywords.pdbx_keywords   OXIDOREDUCTASE 
_struct_keywords.pdbx_details    ? 
# 
_em_3d_fitting.id                1 
_em_3d_fitting.entry_id          EMD-46713 
_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-46713 
_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                  3.8 
_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               146371 
_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            7.6 
# 
_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                 
'S. thermophilus class III ribonucleotide reductase dimer with allosteric effectors ATP and TTP' 
_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 
_em_entity_assembly.mutant_flag          ? 
_em_entity_assembly.chimera              NO 
# 
_em_imaging.entry_id                        EMD-46713 
_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                'FEI TITAN KRIOS' 
_em_imaging.specimen_holder_type            ? 
_em_imaging.specimen_holder_model           ? 
_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             750 
_em_imaging.nominal_defocus_max             2500 
_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             ? 
_em_imaging.c2_aperture_diameter            ? 
_em_imaging.specimen_id                     1 
_em_imaging.cryogen                         ? 
# 
_em_vitrification.entry_id                EMD-46713 
_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-46713 
_em_experiment.id                      1 
_em_experiment.reconstruction_method   'SINGLE PARTICLE' 
_em_experiment.aggregation_state       PARTICLE 
_em_experiment.entity_assembly_id      1 
# 
_em_admin.current_status        REL 
_em_admin.deposition_date       2024-08-23 
_em_admin.deposition_site       RCSB 
_em_admin.details               ? 
_em_admin.entry_id              EMD-46713 
_em_admin.last_update           2025-12-24 
_em_admin.map_release_date      2025-12-17 
_em_admin.header_release_date   2025-12-17 
_em_admin.obsoleted_date        ? 
_em_admin.title                 'S. thermophilus class III ribonucleotide reductase focused refined core' 
_em_admin.process_site          RCSB 
_em_admin.composite_map         NO 
# 
loop_
_em_author_list.author 
_em_author_list.identifier_ORCID 
_em_author_list.ordinal 
'Andree, G.A.'  0000-0002-5620-6951 1 
'Drennan, C.L.' 0000-0001-5486-2755 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                              'PHASE FLIPPING AND AMPLITUDE CORRECTION' 
# 
_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          1308 
_em_entity_assembly_naturalsource.organism             'Streptococcus thermophilus' 
_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         51.35 
_em_image_recording.details                             ? 
_em_image_recording.detector_mode                       ? 
_em_image_recording.film_or_detector_model              'GATAN K3 BIOQUANTUM (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 
? X Y Z 212.992 212.992 212.992 90.0 90.0 90.0 0.00462 author 'Image stored as floating point number (4 bytes)' 256 256 256 big 
emd_46713.map.gz            CCP4 1 1 EMD-46713 ::::EMDATABANK.org::::EMD-46713:::: 255 255 255 0 0 0 0.832 0.832 0.832 67109888 
256 256 256 3.251364E-5  0.020472365 -0.00663929  7.6919975E-4 1 'primary map' 
? X Y Z 212.992 212.992 212.992 90.0 90.0 90.0 0.00671 author 'Image stored as floating point number (4 bytes)' 256 256 256 big 
emd_46713_half_map_1.map.gz CCP4 2 1 EMD-46713 ::::EMDATABANK.org::::EMD-46713:::: 255 255 255 0 0 0 0.832 0.832 0.832 67109888 
256 256 256 3.260708E-5  0.025649317 -0.013790923 0.0011178622 1 'half map'    
? X Y Z 212.992 212.992 212.992 90.0 90.0 90.0 0.0066  author 'Image stored as floating point number (4 bytes)' 256 256 256 big 
emd_46713_half_map_2.map.gz CCP4 3 2 EMD-46713 ::::EMDATABANK.org::::EMD-46713:::: 255 255 255 0 0 0 0.832 0.832 0.832 67109888 
256 256 256 3.2474385E-5 0.023861933 -0.013207851 0.0011001988 1 'half 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 
'PARTICLE SELECTION'       ? 1  1 ? ? ?      ?           
'MODEL REFINEMENT'         ? 2  ? ? ? PHENIX 1.21.1_5286 
'IMAGE ACQUISITION'        ? 3  ? ? 1 ?      ?           
MASKING                    ? 4  ? ? ? ?      ?           
'CTF CORRECTION'           ? 5  1 ? ? RELION 4.0.0       
'LAYERLINE INDEXING'       ? 6  ? ? ? ?      ?           
'DIFFRACTION INDEXING'     ? 7  ? ? ? ?      ?           
'MODEL FITTING'            ? 8  ? ? ? ?      ?           
OTHER                      ? 9  ? ? ? ?      ?           
'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? RELION 4.0.0       
'FINAL EULER ASSIGNMENT'   ? 11 1 ? ? RELION 4.0.0       
CLASSIFICATION             ? 12 1 ? ? ?      ?           
RECONSTRUCTION             ? 13 1 ? ? RELION 4.0.0       
# 
_em_specimen.concentration           ? 
_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 
# 
loop_
_pdbx_audit_support.funding_organization 
_pdbx_audit_support.country 
_pdbx_audit_support.grant_number 
_pdbx_audit_support.details 
_pdbx_audit_support.ordinal 
'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)'      'United States' GM126982    ? 1 
'National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)' 'United States' T32ES007020 ? 2 
'Howard Hughes Medical Institute (HHMI)'                                                        'United States' ?           ? 3 
# 
