data_EMD-14410
# 
_entry.id   EMD-14410 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.382 
_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_1292120169 ? ? 
EMDB  EMD-14410    ? ? 
# 
_pdbx_database_related.db_name        EMDB 
_pdbx_database_related.details        . 
_pdbx_database_related.db_id          EMD-14410 
_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            Nat.Methods 
_citation.journal_id_ASTM           ? 
_citation.journal_id_CSD            ? 
_citation.journal_id_ISSN           1548-7105 
_citation.journal_full              ? 
_citation.journal_issue             ? 
_citation.journal_volume            20 
_citation.language                  ? 
_citation.page_first                284 
_citation.page_last                 294 
_citation.title                     'Convolutional networks for supervised mining of molecular patterns within cellular context.' 
_citation.year                      2023 
_citation.database_id_CSD           ? 
_citation.pdbx_database_id_DOI      10.1038/s41592-022-01746-2 
_citation.pdbx_database_id_PubMed   36690741 
_citation.pdbx_database_id_patent   ? 
_citation.unpublished_flag          ? 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'de Teresa-Trueba, I.' 1  0000-0002-4691-9501 
primary 'Goetz, S.K.'          2  0000-0002-9903-3667 
primary 'Mattausch, A.'        3  0000-0003-0901-8701 
primary 'Stojanovska, F.'      4  0000-0002-4327-1068 
primary 'Zimmerli, C.E.'       5  0000-0003-4388-1349 
primary 'Toro-Nahuelpan, M.'   6  0000-0001-5333-3640 
primary 'Cheng, D.W.C.'        7  ?                   
primary 'Tollervey, F.'        8  ?                   
primary 'Pape, C.'             9  0000-0001-6562-7187 
primary 'Beck, M.'             10 0000-0002-7397-1321 
primary 'Diz-Munoz, A.'        11 ?                   
primary 'Kreshuk, A.'          12 0000-0003-1334-6388 
primary 'Mahamid, J.'          13 0000-0001-6968-041X 
primary 'Zaugg, J.B.'          14 0000-0001-8324-4040 
# 
_exptl.entry_id         EMD-14410 
_exptl.details          ? 
_exptl.method           'ELECTRON MICROSCOPY' 
_exptl.method_details   ? 
# 
_struct_keywords.entry_id        EMD-14410 
_struct_keywords.text            '80S ribosome, RIBOSOME' 
_struct_keywords.pdbx_keywords   RIBOSOME 
_struct_keywords.pdbx_details    ? 
# 
_em_3d_fitting.entry_id          EMD-14410 
_em_3d_fitting.id                1 
_em_3d_fitting.details           ? 
_em_3d_fitting.overall_b_value   ? 
_em_3d_fitting.ref_protocol      ? 
_em_3d_fitting.ref_space         ? 
_em_3d_fitting.target_criteria   ? 
_em_3d_fitting.method            ? 
# 
_em_3d_reconstruction.entry_id                    EMD-14410 
_em_3d_reconstruction.id                          1 
_em_3d_reconstruction.algorithm                   ? 
_em_3d_reconstruction.details                     ? 
_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.num_class_averages          ? 
_em_3d_reconstruction.num_particles               3482 
_em_3d_reconstruction.resolution                  21 
_em_3d_reconstruction.resolution_method           'FSC 0.143 CUT-OFF' 
_em_3d_reconstruction.symmetry_type               POINT 
_em_3d_reconstruction.method                      ? 
_em_3d_reconstruction.nominal_pixel_size          ? 
_em_3d_reconstruction.actual_pixel_size           ? 
_em_3d_reconstruction.magnification_calibration   ? 
# 
_em_buffer.id            1 
_em_buffer.details       ? 
_em_buffer.pH            7 
_em_buffer.specimen_id   1 
_em_buffer.name          ? 
# 
_em_entity_assembly.id                   1 
_em_entity_assembly.parent_id            0 
_em_entity_assembly.details              ? 
_em_entity_assembly.go_id                ? 
_em_entity_assembly.name                 
'80S ribosome with additional density close to the head of the small subunit inside S. pombe cells' 
_em_entity_assembly.source               NATURAL 
_em_entity_assembly.type                 COMPLEX 
_em_entity_assembly.chimera              NO 
_em_entity_assembly.entity_id_list       ? 
_em_entity_assembly.ipr_id               ? 
_em_entity_assembly.synonym              ? 
_em_entity_assembly.number_of_copies     ? 
_em_entity_assembly.oligomeric_details   ? 
# 
_em_imaging.id                              1 
_em_imaging.entry_id                        EMD-14410 
_em_imaging.accelerating_voltage            300 
_em_imaging.alignment_procedure             ? 
_em_imaging.c2_aperture_diameter            ? 
_em_imaging.calibrated_defocus_max          ? 
_em_imaging.calibrated_defocus_min          ? 
_em_imaging.calibrated_magnification        ? 
_em_imaging.cryogen                         ? 
_em_imaging.details                         ? 
_em_imaging.electron_source                 'FIELD EMISSION GUN' 
_em_imaging.illumination_mode               'FLOOD BEAM' 
_em_imaging.microscope_model                'TFS KRIOS' 
_em_imaging.mode                            'BRIGHT FIELD' 
_em_imaging.nominal_cs                      ? 
_em_imaging.nominal_defocus_max             4000 
_em_imaging.nominal_defocus_min             2000 
_em_imaging.nominal_magnification           42000 
_em_imaging.recording_temperature_maximum   ? 
_em_imaging.recording_temperature_minimum   ? 
_em_imaging.residual_tilt                   ? 
_em_imaging.specimen_holder_model           ? 
_em_imaging.specimen_id                     1 
_em_imaging.sample_support_id               1 
_em_imaging.citation_id                     ? 
_em_imaging.detector_id                     1 
_em_imaging.scans_id                        1 
_em_imaging.date                            ? 
_em_imaging.temperature                     ? 
_em_imaging.tilt_angle_min                  ? 
_em_imaging.tilt_angle_max                  ? 
_em_imaging.astigmatism                     ? 
_em_imaging.detector_distance               ? 
_em_imaging.electron_beam_tilt_params       ? 
_em_imaging.specimen_holder_type            ? 
# 
_em_sample_support.id               1 
_em_sample_support.specimen_id      1 
_em_sample_support.details          ? 
_em_sample_support.grid_material    COPPER 
_em_sample_support.grid_mesh_size   200 
_em_sample_support.grid_type        'Quantifoil R2/1' 
_em_sample_support.method           ? 
_em_sample_support.film_material    ? 
# 
_em_vitrification.id                      1 
_em_vitrification.specimen_id             1 
_em_vitrification.chamber_temperature     ? 
_em_vitrification.cryogen_name            ETHANE 
_em_vitrification.details                 ? 
_em_vitrification.humidity                ? 
_em_vitrification.instrument              ? 
_em_vitrification.entry_id                EMD-14410 
_em_vitrification.sample_preparation_id   ? 
_em_vitrification.citation_id             ? 
_em_vitrification.method                  ? 
_em_vitrification.temp                    ? 
_em_vitrification.time_resolved_state     ? 
# 
_em_experiment.entry_id                EMD-14410 
_em_experiment.id                      1 
_em_experiment.aggregation_state       CELL 
_em_experiment.reconstruction_method   'SUBTOMOGRAM AVERAGING' 
_em_experiment.entity_assembly_id      1 
# 
_em_single_particle_entity.entry_id              EMD-14410 
_em_single_particle_entity.id                    1 
_em_single_particle_entity.image_processing_id   1 
_em_single_particle_entity.point_symmetry        C1 
# 
_em_admin.entry_id              EMD-14410 
_em_admin.current_status        REL 
_em_admin.deposition_date       2022-02-22 
_em_admin.deposition_site       PDBE 
_em_admin.details               ? 
_em_admin.last_update           2023-12-13 
_em_admin.map_release_date      2022-11-16 
_em_admin.obsoleted_date        ? 
_em_admin.title                 
;Subtomogram average of S. pombe 80S ribosomes with an additional density close to the head of the small subunit from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae
;
_em_admin.header_release_date   2022-11-16 
# 
loop_
_em_author_list.ordinal 
_em_author_list.author 
_em_author_list.identifier_ORCID 
1 'Mahamid, J.' 0000-0001-6968-041X 
2 'Goetz, S.K.' 0000-0002-9903-3667 
# 
_em_ctf_correction.id                                1 
_em_ctf_correction.em_image_processing_id            1 
_em_ctf_correction.type                              'PHASE FLIPPING AND AMPLITUDE CORRECTION' 
_em_ctf_correction.details                           ? 
_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.phase_reversal                    ? 
_em_ctf_correction.phase_reversal_anisotropic        ? 
_em_ctf_correction.phase_reversal_correction_space   ? 
# 
_em_entity_assembly_molwt.entity_assembly_id   1 
_em_entity_assembly_molwt.id                   1 
_em_entity_assembly_molwt.experimental_flag    NO 
_em_entity_assembly_molwt.units                ? 
_em_entity_assembly_molwt.value                ? 
# 
_em_entity_assembly_naturalsource.id                   2 
_em_entity_assembly_naturalsource.entity_assembly_id   1 
_em_entity_assembly_naturalsource.cell                 ? 
_em_entity_assembly_naturalsource.cellular_location    cytoplasm 
_em_entity_assembly_naturalsource.ncbi_tax_id          4896 
_em_entity_assembly_naturalsource.organ                ? 
_em_entity_assembly_naturalsource.organelle            ? 
_em_entity_assembly_naturalsource.organism             'Schizosaccharomyces pombe' 
_em_entity_assembly_naturalsource.strain               ? 
_em_entity_assembly_naturalsource.tissue               ? 
# 
loop_
_em_euler_angle_assignment.id 
_em_euler_angle_assignment.details 
_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 ? ? ? 'NOT APPLICABLE'     
2 ? 1 FINAL   ? ? ? 'MAXIMUM LIKELIHOOD' 
# 
_em_final_classification.id                         1 
_em_final_classification.type                       3D 
_em_final_classification.avg_num_images_per_class   ? 
_em_final_classification.details                    ? 
_em_final_classification.image_processing_id        1 
_em_final_classification.num_classes                ? 
# 
_em_grid_pretreatment.id                  1 
_em_grid_pretreatment.sample_support_id   1 
_em_grid_pretreatment.atmosphere          ? 
_em_grid_pretreatment.pressure            ? 
_em_grid_pretreatment.time                ? 
_em_grid_pretreatment.type                'GLOW DISCHARGE' 
# 
_em_image_processing.id                   1 
_em_image_processing.image_recording_id   1 
_em_image_processing.details              ? 
# 
_em_image_recording.id                                  1 
_em_image_recording.imaging_id                          1 
_em_image_recording.avg_electron_dose_per_image         2.2 
_em_image_recording.average_exposure_time               ? 
_em_image_recording.details                             ? 
_em_image_recording.detector_mode                       COUNTING 
_em_image_recording.film_or_detector_model              'GATAN K2 SUMMIT (4k x 4k)' 
_em_image_recording.num_diffraction_images              ? 
_em_image_recording.num_grids_imaged                    ? 
_em_image_recording.num_real_images                     ? 
_em_image_recording.avg_electron_dose_per_subtomogram   113.6 
# 
_em_imaging_optics.id                         1 
_em_imaging_optics.imaging_id                 1 
_em_imaging_optics.chr_aberration_corrector   ? 
_em_imaging_optics.energyfilter_lower         ? 
_em_imaging_optics.energyfilter_name          'GIF Quantum LS' 
_em_imaging_optics.energyfilter_upper         ? 
_em_imaging_optics.energyfilter_slit_width    20 
_em_imaging_optics.phase_plate                'VOLTA PHASE PLATE' 
_em_imaging_optics.sph_aberration_corrector   ? 
_em_imaging_optics.details                    ? 
# 
_em_map.entry_id               EMD-14410 
_em_map.id                     1 
_em_map.annotation_details     
;Subtomogram average of 80S ribosomes with an additional density close to the head of the small subunit from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae of S. pombe
;
_em_map.axis_order_fast        X 
_em_map.axis_order_medium      Y 
_em_map.axis_order_slow        Z 
_em_map.cell_a                 471.828 
_em_map.cell_alpha             90.0 
_em_map.cell_b                 471.828 
_em_map.cell_beta              90.0 
_em_map.cell_c                 471.828 
_em_map.cell_gamma             90.0 
_em_map.contour_level          0.07 
_em_map.contour_level_source   author 
_em_map.data_type              'Image stored as floating point number (4 bytes)' 
_em_map.dimensions_col         140 
_em_map.dimensions_row         140 
_em_map.dimensions_sec         140 
_em_map.endian_type            big 
_em_map.file                   emd_14410.map.gz 
_em_map.format                 CCP4 
_em_map.label                  ::::EMDATABANK.org::::EMD-14410:::: 
_em_map.limit_col              139 
_em_map.limit_row              139 
_em_map.limit_sec              139 
_em_map.origin_col             0 
_em_map.origin_row             0 
_em_map.origin_sec             0 
_em_map.partition              1 
_em_map.pixel_spacing_x        3.3702 
_em_map.pixel_spacing_y        3.3702 
_em_map.pixel_spacing_z        3.3702 
_em_map.size_kb                10977024 
_em_map.spacing_x              140 
_em_map.spacing_y              140 
_em_map.spacing_z              140 
_em_map.statistics_average     0.004338604 
_em_map.statistics_maximum     0.4613201 
_em_map.statistics_minimum     -0.31389123 
_em_map.statistics_std         0.054735884 
_em_map.symmetry_space_group   1 
_em_map.type                   'primary map' 
# 
loop_
_em_software.id 
_em_software.category 
_em_software.details 
_em_software.name 
_em_software.version 
_em_software.image_processing_id 
_em_software.fitting_id 
_em_software.imaging_id 
1  'VOLUME SELECTION'         ? Warp     ? 1 ? ? 
2  'IMAGE ACQUISITION'        ? SerialEM ? ? ? 1 
3  MASKING                    ? ?        ? ? ? ? 
4  'CTF CORRECTION'           ? Warp     ? 1 ? ? 
5  'LAYERLINE INDEXING'       ? ?        ? ? ? ? 
6  'DIFFRACTION INDEXING'     ? ?        ? ? ? ? 
7  'MODEL FITTING'            ? ?        ? ? ? ? 
8  'MODEL REFINEMENT'         ? ?        ? ? ? ? 
9  OTHER                      ? ?        ? ? ? ? 
10 'INITIAL EULER ASSIGNMENT' ? ?        ? 1 ? ? 
11 'FINAL EULER ASSIGNMENT'   ? RELION   ? 1 ? ? 
12 CLASSIFICATION             ? RELION   ? 1 ? ? 
13 RECONSTRUCTION             ? RELION   ? 1 ? ? 
# 
_em_specimen.id                      1 
_em_specimen.experiment_id           1 
_em_specimen.concentration           ? 
_em_specimen.details                 ? 
_em_specimen.embedding_applied       NO 
_em_specimen.shadowing_applied       NO 
_em_specimen.staining_applied        NO 
_em_specimen.vitrification_applied   YES 
# 
_em_support_film.id                  1 
_em_support_film.sample_support_id   1 
_em_support_film.material            CARBON 
_em_support_film.thickness           ? 
_em_support_film.topology            HOLEY 
# 
_em_tomography.id                        1 
_em_tomography.imaging_id                1 
_em_tomography.axis1_angle_increment     2 
_em_tomography.axis1_max_angle           58 
_em_tomography.axis1_min_angle           -50 
_em_tomography.axis2_angle_increment     ? 
_em_tomography.axis2_max_angle           ? 
_em_tomography.axis2_min_angle           ? 
_em_tomography.dual_tilt_axis_rotation   ? 
# 
_em_volume_selection.id                      1 
_em_volume_selection.details                 ? 
_em_volume_selection.image_processing_id     1 
_em_volume_selection.method                  ? 
_em_volume_selection.num_tomograms           10 
_em_volume_selection.num_volumes_extracted   25311 
_em_volume_selection.reference_model         ? 
# 
_pdbx_audit_support.funding_organization   'European Research Council (ERC)' 
_pdbx_audit_support.country                'European Union' 
_pdbx_audit_support.grant_number           760067 
_pdbx_audit_support.details                ? 
_pdbx_audit_support.ordinal                1 
# 
