data_EMD-70586
# 
_entry.id   EMD-70586 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.410 
_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_1000295813 ? ? 
EMDB  EMD-70586    ? ? 
# 
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 2026-03-25 ? 
2 FSC           1 0 2026-03-25 ? 
3 'Half map'    1 0 2026-03-25 1 
4 'Half map'    1 0 2026-03-25 2 
5 Image         1 0 2026-03-25 ? 
6 Mask          1 0 2026-03-25 1 
7 'Primary map' 1 0 2026-03-25 ? 
# 
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 Mask          repository 'Initial release' ? ? 
7 7 'Primary map' repository 'Initial release' ? ? 
# 
_pdbx_database_related.db_name        EMDB 
_pdbx_database_related.details        . 
_pdbx_database_related.db_id          EMD-70586 
_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                   ? 
_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                     
'Cryo-EM Structure of Ryanodine Receptor 1: Drug Bound Open Conformation BSol Locally Refined Map' 
_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 'Molinarolo, S.M.' 1 0000-0002-6077-1291 
primary 'Van Petegem, F.'  2 0000-0003-2728-8537 
# 
_exptl.entry_id         EMD-70586 
_exptl.details          ? 
_exptl.method           'ELECTRON MICROSCOPY' 
_exptl.method_details   ? 
# 
_struct_keywords.entry_id        EMD-70586 
_struct_keywords.text            'Ion channel, Calcium Channel, TRANSPORT PROTEIN' 
_struct_keywords.pdbx_keywords   'TRANSPORT PROTEIN' 
_struct_keywords.pdbx_details    ? 
# 
_em_3d_fitting.id                1 
_em_3d_fitting.entry_id          EMD-70586 
_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      'RIGID BODY FIT' 
# 
_em_3d_fitting_list.id                            1 
_em_3d_fitting_list.3d_fitting_id                 1 
_em_3d_fitting_list.pdb_entry_id                  7TZC 
_em_3d_fitting_list.pdb_chain_id                  A 
_em_3d_fitting_list.pdb_chain_residue_range       1-5037 
_em_3d_fitting_list.details                       ? 
_em_3d_fitting_list.chain_id                      A 
_em_3d_fitting_list.chain_residue_range           1-5037 
_em_3d_fitting_list.source_name                   PDB 
_em_3d_fitting_list.type                          'experimental model' 
_em_3d_fitting_list.accession_code                7TZC 
_em_3d_fitting_list.initial_refinement_model_id   1 
# 
_em_3d_reconstruction.entry_id                    EMD-70586 
_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                  3.35 
_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               694588 
_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            7.5 
# 
_em_entity_assembly.id                   1 
_em_entity_assembly.parent_id            0 
_em_entity_assembly.source               NATURAL 
_em_entity_assembly.type                 'ORGANELLE OR CELLULAR COMPONENT' 
_em_entity_assembly.name                 'Tetrameric complex of RyR1 with FKBP12.6' 
_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' 
_em_entity_assembly.mutant_flag          ? 
_em_entity_assembly.chimera              NO 
# 
_em_imaging.entry_id                        EMD-70586 
_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                            'DARK FIELD' 
_em_imaging.nominal_cs                      2.7 
_em_imaging.nominal_defocus_min             500 
_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                         NITROGEN 
_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   300 
_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-70586 
_em_vitrification.id                      1 
_em_vitrification.sample_preparation_id   ? 
_em_vitrification.specimen_id             1 
_em_vitrification.cryogen_name            ETHANE 
_em_vitrification.humidity                100 
_em_vitrification.temp                    ? 
_em_vitrification.chamber_temperature     277.15 
_em_vitrification.instrument              'FEI VITROBOT MARK IV' 
_em_vitrification.method                  ? 
_em_vitrification.time_resolved_state     ? 
_em_vitrification.citation_id             ? 
_em_vitrification.details                 ? 
# 
_em_experiment.entry_id                EMD-70586 
_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       2025-05-12 
_em_admin.deposition_site       RCSB 
_em_admin.details               ? 
_em_admin.entry_id              EMD-70586 
_em_admin.last_update           2026-03-25 
_em_admin.map_release_date      2026-03-25 
_em_admin.header_release_date   2026-03-25 
_em_admin.obsoleted_date        ? 
_em_admin.title                 'Cryo-EM Structure of Ryanodine Receptor 1: Drug Bound Open Conformation BSol Locally Refined Map' 
_em_admin.process_site          RCSB 
_em_admin.composite_map         NO 
# 
loop_
_em_author_list.author 
_em_author_list.identifier_ORCID 
_em_author_list.ordinal 
'Molinarolo, S.M.' 0000-0002-6077-1291 1 
'Van Petegem, F.'  0000-0003-2728-8537 2 
# 
loop_
_em_buffer_component.buffer_id 
_em_buffer_component.concentration 
_em_buffer_component.concentration_units 
_em_buffer_component.formula 
_em_buffer_component.id 
_em_buffer_component.name 
1 10    mM ? 1  Atorvastatin      
1 2     %  ? 2  DMSO              
1 2     mM ? 3  Caffeine          
1 36    uM ? 4  'Free Ca2+'       
1 2     mM ? 5  EGTA              
1 25    mM ? 6  Tris              
1 250   mM ? 7  'Sodium Chloride' 
1 0.5   mM ? 8  TCEP              
1 0.5   mM ? 9  Benzamidine       
1 0.375 %  ? 10 CHAPS             
1 0.001 %  ? 11 DOPC              
# 
_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_molwt.entity_assembly_id   1 
_em_entity_assembly_molwt.experimental_flag    NO 
_em_entity_assembly_molwt.id                   1 
_em_entity_assembly_molwt.units                MEGADALTONS 
_em_entity_assembly_molwt.value                2.39 
_em_entity_assembly_molwt.method               ? 
# 
_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          9986 
_em_entity_assembly_naturalsource.organism             'Oryctolagus cuniculus' 
_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              ? 
# 
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_final_classification.avg_num_images_per_class   ? 
_em_final_classification.details                    ? 
_em_final_classification.id                         1 
_em_final_classification.image_processing_id        1 
_em_final_classification.num_classes                ? 
_em_final_classification.type                       3D 
# 
_em_grid_pretreatment.atmosphere          Air 
_em_grid_pretreatment.id                  1 
_em_grid_pretreatment.pressure            0.039 
_em_grid_pretreatment.sample_support_id   1 
_em_grid_pretreatment.time                25 
_em_grid_pretreatment.type                'GLOW DISCHARGE' 
# 
_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              'FEI FALCON IV (4k 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                    3 
_em_image_recording.num_real_images                     35751 
# 
_em_imaging_optics.chr_aberration_corrector   ? 
_em_imaging_optics.energyfilter_lower         ? 
_em_imaging_optics.energyfilter_slit_width    ? 
_em_imaging_optics.energyfilter_name          'TFS Selectris' 
_em_imaging_optics.energyfilter_upper         ? 
_em_imaging_optics.id                         1 
_em_imaging_optics.imaging_id                 1 
_em_imaging_optics.phase_plate                ? 
_em_imaging_optics.sph_aberration_corrector   ? 
_em_imaging_optics.details                    ? 
# 
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 
'Local Refinement BSol'        X Y Z 491.52 491.52 491.52 90.0 90.0 90.0 0.155 author 
'Image stored as floating point number (4 bytes)' 512 512 512 big emd_70586.map.gz            CCP4 1 1 EMD-70586 
::::EMDATABANK.org::::EMD-70586:::: 511 511 511 0 0 0 0.96 0.96 0.96 536871936 512 512 512 0.0013742205 0.5435762  -0.2172999  
0.010398157 1 'primary map' 
'Local Refinement BSol Half A' X Y Z 491.52 491.52 491.52 90.0 90.0 90.0 0.155 author 
'Image stored as floating point number (4 bytes)' 512 512 512 big emd_70586_half_map_1.map.gz CCP4 2 1 EMD-70586 
::::EMDATABANK.org::::EMD-70586:::: 511 511 511 0 0 0 0.96 0.96 0.96 536871936 512 512 512 8.180385E-4  0.5858545  -0.23393941 
0.019524012 1 'half map'    
'Local Refinement BSol Half B' X Y Z 491.52 491.52 491.52 90.0 90.0 90.0 0.155 author 
'Image stored as floating point number (4 bytes)' 512 512 512 big emd_70586_half_map_2.map.gz CCP4 3 2 EMD-70586 
::::EMDATABANK.org::::EMD-70586:::: 511 511 511 0 0 0 0.96 0.96 0.96 536871936 512 512 512 8.143062E-4  0.59154326 -0.23053987 
0.019564237 1 'half map'    
'Local Refinement BSol Mask'   X Y Z 491.52 491.52 491.52 90.0 90.0 90.0 0.155 author 
'Image stored as floating point number (4 bytes)' 512 512 512 big emd_70586_msk_1.map         CCP4 4 1 EMD-70586 
::::EMDATABANK.org::::EMD-70586:::: 511 511 511 0 0 0 0.96 0.96 0.96 536871936 512 512 512 0.00788985   1.0        0.0         
0.080755375 1 mask          
# 
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 ? ? Topaz     0.2.3  ? 
'IMAGE ACQUISITION'        ? 2  ? ? 1 ?         ?      ? 
MASKING                    ? 3  ? ? ? ?         ?      ? 
'CTF CORRECTION'           ? 4  1 ? ? cryoSPARC 4.4.1  ? 
'LAYERLINE INDEXING'       ? 5  ? ? ? ?         ?      ? 
'DIFFRACTION INDEXING'     ? 6  ? ? ? ?         ?      ? 
'MODEL FITTING'            ? 7  ? 1 ? PHENIX    1.21.1 ? 
OTHER                      ? 8  ? ? ? ?         ?      ? 
'MODEL REFINEMENT'         ? 9  ? 1 ? PHENIX    1.21.1 ? 
'MODEL REFINEMENT'         ? 10 ? 1 ? ISOLDE    1.7.1  ? 
'INITIAL EULER ASSIGNMENT' ? 11 1 ? ? cryoSPARC 4.4.1  ? 
'FINAL EULER ASSIGNMENT'   ? 12 1 ? ? cryoSPARC 4.4.1  ? 
CLASSIFICATION             ? 13 1 ? ? cryoSPARC 4.4.1  ? 
RECONSTRUCTION             ? 14 1 ? ? cryoSPARC 4.4.1  ? 
# 
_em_specimen.concentration           10 
_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                           7TZC 
_em_start_model.random_conical_tilt_angle        ? 
_em_start_model.random_conical_tilt_num_images   ? 
_em_start_model.type                             'PDB ENTRY' 
# 
_em_support_film.id                  1 
_em_support_film.material            CARBON 
_em_support_film.sample_support_id   1 
_em_support_film.thickness           ? 
_em_support_film.topology            HOLEY 
# 
_pdbx_audit_support.funding_organization   'Canadian Institutes of Health Research (CIHR)' 
_pdbx_audit_support.country                Canada 
_pdbx_audit_support.grant_number           ? 
_pdbx_audit_support.details                ? 
_pdbx_audit_support.ordinal                1 
# 
_pdbx_initial_refinement_model.id               1 
_pdbx_initial_refinement_model.type             'experimental model' 
_pdbx_initial_refinement_model.source_name      PDB 
_pdbx_initial_refinement_model.accession_code   7TZC 
# 
