data_EMD-73263
# 
_entry.id   EMD-73263 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.412 
_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_1000300997 ? ? 
EMDB  EMD-73263    ? ? 
# 
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 2026-03-18 ? 
2 FSC           1 0 2026-03-18 ? 
3 'Half map'    1 0 2026-03-18 1 
4 'Half map'    1 0 2026-03-18 2 
5 Image         1 0 2026-03-18 ? 
6 'Primary map' 1 0 2026-03-18 ? 
# 
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 FSC           repository 'Initial release' ? ? 
3 3 'Half map'    repository 'Initial release' ? ? 
4 4 'Half map'    repository 'Initial release' ? ? 
5 5 Image         repository 'Initial release' ? ? 
6 6 '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 . EMD-73260 'other EM volume'      
EMDB . EMD-73228 'other EM volume'      
PDB  . 9YOK      unspecified            
PDB  . 9YNR      unspecified            
EMDB . EMD-73245 'other EM volume'      
PDB  . 9YNX      unspecified            
EMDB . EMD-73231 'other EM volume'      
EMDB . EMD-73244 'other EM volume'      
EMDB . EMD-73263 '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            'Plos Pathog.' 
_citation.journal_id_ASTM           ? 
_citation.journal_id_CSD            ? 
_citation.journal_id_ISSN           1553-7374 
_citation.journal_full              ? 
_citation.journal_issue             ? 
_citation.journal_volume            22 
_citation.language                  ? 
_citation.page_first                e1014071 
_citation.page_last                 e1014071 
_citation.title                     'Neutralization of SARS-CoV-2 by IgM-14 via engagement of two distinct spike epitopes.' 
_citation.year                      2026 
_citation.database_id_CSD           ? 
_citation.pdbx_database_id_DOI      10.1371/journal.ppat.1014071 
_citation.pdbx_database_id_PubMed   41880376 
_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  ?                   
primary 'Hu, Y.'              2  ?                   
primary 'Ku, Z.'              3  ?                   
primary 'Yeung, J.'           4  ?                   
primary 'Zou, J.'             5  ?                   
primary 'Woodson, M.'         6  ?                   
primary 'Prokhorov, N.S.'     7  ?                   
primary 'Knyazhanskaya, E.S.' 8  ?                   
primary 'Zhao, H.'            9  ?                   
primary 'Sherman, M.B.'       10 ?                   
primary 'An, Z.'              11 ?                   
primary 'Carroll, S.F.'       12 ?                   
primary 'Shi, P.Y.'           13 ?                   
primary 'Leiman, P.G.'        14 ?                   
primary 'Xie, X.'             15 0000-0003-0918-016X 
# 
_exptl.entry_id         EMD-73263 
_exptl.details          ? 
_exptl.method           'ELECTRON MICROSCOPY' 
_exptl.method_details   ? 
# 
_struct_keywords.entry_id        EMD-73263 
_struct_keywords.text            'SARS-CoV-2, neutralizing antibody, VIRAL PROTEIN' 
_struct_keywords.pdbx_keywords   'VIRAL PROTEIN' 
_struct_keywords.pdbx_details    ? 
# 
_em_3d_fitting.id                1 
_em_3d_fitting.entry_id          EMD-73263 
_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-73263 
_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                  3.48 
_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               52375 
_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            8 
# 
_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                 'Fab-14/SARS-CoV-2 D614G spike complex' 
_em_entity_assembly.details              'Mode I, subgroup I, 1-Fab-14 bind to 1-up-RBD' 
_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       ? 
_em_entity_assembly.mutant_flag          ? 
_em_entity_assembly.chimera              NO 
# 
_em_imaging.entry_id                        EMD-73263 
_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           ? 
_em_imaging.details                         ? 
_em_imaging.date                            ? 
_em_imaging.accelerating_voltage            300 
_em_imaging.illumination_mode               'SPOT SCAN' 
_em_imaging.mode                            DIFFRACTION 
_em_imaging.nominal_cs                      ? 
_em_imaging.nominal_defocus_min             1000 
_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           10500 
_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_imaging.objective_aperture              ? 
_em_imaging.microscope_serial_number        ? 
_em_imaging.microscope_version              ? 
# 
_em_sample_support.id               1 
_em_sample_support.film_material    ? 
_em_sample_support.method           ? 
_em_sample_support.grid_material    COPPER 
_em_sample_support.grid_mesh_size   ? 
_em_sample_support.grid_type        'Quantifoil R2/2' 
_em_sample_support.pretreatment     ? 
_em_sample_support.details          ? 
_em_sample_support.specimen_id      1 
_em_sample_support.citation_id      ? 
# 
_em_vitrification.entry_id                EMD-73263 
_em_vitrification.id                      1 
_em_vitrification.sample_preparation_id   ? 
_em_vitrification.specimen_id             1 
_em_vitrification.cryogen_name            ETHANE 
_em_vitrification.humidity                95 
_em_vitrification.temp                    ? 
_em_vitrification.chamber_temperature     295 
_em_vitrification.instrument              'LEICA EM GP' 
_em_vitrification.method                  ? 
_em_vitrification.time_resolved_state     ? 
_em_vitrification.citation_id             ? 
_em_vitrification.details                 ? 
# 
_em_experiment.entry_id                EMD-73263 
_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       2025-10-13 
_em_admin.deposition_site       RCSB 
_em_admin.details               ? 
_em_admin.entry_id              EMD-73263 
_em_admin.last_update           2026-04-08 
_em_admin.map_release_date      2026-03-18 
_em_admin.header_release_date   2026-03-18 
_em_admin.obsoleted_date        ? 
_em_admin.title                 'Fab-14/SARS-CoV-2 D614G spike complex, Mode II, subgroup I conformation' 
_em_admin.process_site          RCSB 
_em_admin.composite_map         NO 
# 
loop_
_em_author_list.author 
_em_author_list.identifier_ORCID 
_em_author_list.ordinal 
'Wang, Y.'   ? 1 
'Hu, Y.'     ? 2 
'Leiman, P.' ? 3 
'Xie, X.'    ? 4 
# 
_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          2697049 
_em_entity_assembly_naturalsource.organism             'Severe acute respiratory syndrome coronavirus 2' 
_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          9606 
_em_entity_assembly_recombinant.organism             'Homo sapiens' 
_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_grid_pretreatment.atmosphere          ? 
_em_grid_pretreatment.id                  1 
_em_grid_pretreatment.pressure            ? 
_em_grid_pretreatment.sample_support_id   1 
_em_grid_pretreatment.time                ? 
_em_grid_pretreatment.type                'PLASMA CLEANING' 
# 
_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         43.17 
_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 
?            X Y Z 352.338 352.338 352.338 90.0 90.0 90.0 0.003 author 'Image stored as floating point number (4 bytes)' 420 420 
420 big emd_73263.map.gz            CCP4 1 1 EMD-73263 ::::EMDATABANK.org::::EMD-73263:::: 419 419 419 0 0 0 0.8389 0.8389 0.8389 
296353024 420 420 420 6.46844E-5   0.026235832 -0.010455005 6.5430184E-4 1 'primary map' 
'half map A' X Y Z 352.338 352.338 352.338 90.0 90.0 90.0 0.004 author 'Image stored as floating point number (4 bytes)' 420 420 
420 big emd_73263_half_map_1.map.gz CCP4 2 1 EMD-73263 ::::EMDATABANK.org::::EMD-73263:::: 419 419 419 0 0 0 0.8389 0.8389 0.8389 
296353024 420 420 420 6.2327425E-5 0.04415202  -0.027323788 0.0011272685 1 'half map'    
'half map B' X Y Z 352.338 352.338 352.338 90.0 90.0 90.0 0.004 author 'Image stored as floating point number (4 bytes)' 420 420 
420 big emd_73263_half_map_2.map.gz CCP4 3 2 EMD-73263 ::::EMDATABANK.org::::EMD-73263:::: 419 419 419 0 0 0 0.8389 0.8389 0.8389 
296353024 420 420 420 6.236179E-5  0.042816497 -0.03130334  0.0011159917 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 
_em_software.reference_DOI 
'PARTICLE SELECTION'            ?                             1  1 ? ? cryoSPARC ? ? 
'IMAGE ACQUISITION'             ?                             2  ? ? 1 ?         ? ? 
MASKING                         ?                             3  ? ? ? ?         ? ? 
'CTF CORRECTION'                ?                             4  1 ? ? ?         ? ? 
'LAYERLINE INDEXING'            ?                             5  ? ? ? ?         ? ? 
'DIFFRACTION INDEXING'          ?                             6  ? ? ? ?         ? ? 
'MODEL FITTING'                 ?                             7  ? ? ? ?         ? ? 
'MODEL REFINEMENT'              ?                             8  ? ? ? ?         ? ? 
OTHER                           ?                             9  ? ? ? ?         ? ? 
'INITIAL EULER ASSIGNMENT'      ?                             10 1 ? ? ?         ? ? 
'FINAL EULER ASSIGNMENT'        ?                             11 1 ? ? ?         ? ? 
CLASSIFICATION                  ?                             12 1 ? ? ?         ? ? 
RECONSTRUCTION                  '3D Flex refinement is used.' 13 1 ? ? cryoSPARC ? ? 
'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           0.3 
_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                             OTHER 
# 
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' R01GM139034 ? 1 
'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' R35GM158090 ? 2 
# 
