Information Specific To Electron Microscopy (3DEM)

Sample Description

PDBx/mmCIF category	Legacy PDB format records	Description
_em_entity_assembly	REMARK 245	Details about each component of the complex.

Notes:

An isolated protein would be classified in _em_entity_assembly.type as "COMPLEX". The other categories refer to large-scale samples, such as "CELL", "VIRUS", etc.

Example:

_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	'Core tetramer assembly (p2) of the phiPA3 bacteriophage PhuN protein'
_em_entity_assembly.details	?
_em_entity_assembly.synonym	?
_em_entity_assembly.oligomeric_details	?
_em_entity_assembly.entity_id_list	1

PDBx/mmCIF category	Legacy PDB format records	Description
_em_entity_assembly_molwt	N/A	Details about the molecular weight of an assembly component of the sample.

Example:

loop_
_em_entity_assembly_molwt.entity_assembly_id
_em_entity_assembly_molwt.id
_em_entity_assembly_molwt.units
_em_entity_assembly_molwt.value
1	1	MEGADALTONS	30.5

PDBx/mmCIF category	Legacy PDB format records	Description
_em_entity_assembly_naturalsource	N/A	Details about the natural source for EM assemblies and assembly components.

Example:

_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	998086
_em_entity_assembly_naturalsource.organism	'Pseudomonas phage PhiPA3'
_em_entity_assembly_naturalsource.organelle	?
_em_entity_assembly_naturalsource.organ	?
_em_entity_assembly_naturalsource.strain	?
_em_entity_assembly_naturalsource.tissue	?

PDBx/mmCIF category	Legacy PDB format records	Description
_em_entity_assembly_recombinant	N/A	Details about the recombinant expression of the assembly or assembly component.

Example:

_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	'BL21 Star (DE3)pLysS'

EM Experiment

PDBx/mmCIF category	Legacy PDB format records	Description
_em_experiment	REMARK 245	High-level classification of the EM experiment.

Example:

_em_experiment.entry_id	8FNE
_em_experiment.id	1
_em_experiment.reconstruction_method	'SINGLE PARTICLE'
_em_experiment.aggregation_state	'2D ARRAY'
_em_experiment.entity_assembly_id	1

Sample preparation

PDBx/mmCIF category	Legacy PDB format records	Description
_em_specimen	REMARK 245	Details about specimens prepared for imaging by electron microscopy.

Example:

_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

PDBx/mmCIF category	Legacy PDB format records	Description
_em_buffer	REMARK 245	Details of the sample buffer.

Example:

_em_buffer.id	1
_em_buffer.specimen_id	1
_em_buffer.name	?
_em_buffer.details	'0.25 complete Protease Inhibitor Tablet also included'
_em_buffer.pH	6.5

PDBx/mmCIF category	Legacy PDB format records	Description
_em_buffer_component	N/A	Details of the sample buffer components.

Example:

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	20	mM	?	1	BisTrisPropane
1	150	mM	?	2	'Sodium Chloride'
1	1	mM	?	3	DTT
1	1	mM	?	4	EDTA
1	2	mM	?	5	'Magnesium Chloride'
1	1	mM	?	6	ATP

PDBx/mmCIF category	Legacy PDB format records	Description
_em_staining	N/A	Details about the staining procedure used in the specimen preparation.

Example:

_em_staining.id	1
_em_staining.specimen_id	1
_em_staining.material	'Uranyl Acetate'
_em_staining.type	NEGATIVE
_em_staining.details	'Negatively stained EM specimens were prepared using a carbon-sandwich technique and uranyl-acetate stain.'

PDBx/mmCIF category	Legacy PDB format records	Description
_em_embedding	N/A	Details about the embedding procedure used in the specimen preparation.

Example:

_em_embedding.details	'3% trehalose'
_em_embedding.id	1
_em_embedding.material	trehalose
_em_embedding.specimen_id	1

PDBx/mmCIF category	Legacy PDB format records	Description
_em_shadowing	N/A	Details about the shadowing of an EM specimen.

Example:

_em_shadowing.id	1
_em_shadowing.specimen_id	1
_em_shadowing.angle	45
_em_shadowing.thickness	3
_em_shadowing.material	Platinum
_em_shadowing.details	'shadowing was used to create a platinum replica'

PDBx/mmCIF category	Legacy PDB format records	Description
_em_sample_support	REMARK 245	Details of the electron microscope grid type, grid support film and pretreatment of the whole before sample is applied.

Example:

_em_sample_support.id	1
_em_sample_support.film_material	'HOLEY CARBON'
_em_sample_support.grid_material	COPPER
_em_sample_support.grid_mesh_size	400
_em_sample_support.details	'GLOW DISCHARGED 120 seconds'

PDBx/mmCIF category	Legacy PDB format records	Description
_em_support_film	N/A	Describes films supporting the specimen.

Example:

_em_support_film.id	1
_em_support_film.material	CARBON

PDBx/mmCIF category	Legacy PDB format records	Description
_em_grid_pretreatment	N/A	Describes glow discharge pretreatment for an EM grid.

Example:

_em_grid_pretreatment.id	1
_em_grid_pretreatment.sample_support_id	1
_em_grid_pretreatment.type	'GLOW DISCHARGE'
_em_grid_pretreatment.time	12

PDBx/mmCIF category	Legacy PDB format records	Description
_em_vitrification	REMARK 245	Details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope.

Example:

_em_vitrification.entry_id	8FNE
_em_vitrification.id	1
_em_vitrification.specimen_id	1
_em_vitrification.cryogen_name	ETHANE
_em_vitrification.humidity	100
_em_vitrification.temp	?
_em_vitrification.chamber_temperature	283.15
_em_vitrification.instrument	'FEI VITROBOT MARK IV'
_em_vitrification.method	?
_em_vitrification.time_resolved_state	?
_em_vitrification.citation_id	?
_em_vitrification.details	?

Imaging

PDBx/mmCIF category	Legacy PDB format records	Description
_em_imaging	REMARK 245	Details about the parameters used in imaging the sample in the electron microscope.

Example:

_em_imaging.entry_id	8FNE
_em_imaging.id	1
_em_imaging.microscope_model	'FEI TITAN KRIOS'
_em_imaging.specimen_holder_type	?
_em_imaging.specimen_holder_model	'FEI TITAN KRIOS AUTOGRID HOLDER'
_em_imaging.accelerating_voltage	300
_em_imaging.illumination_mode	'FLOOD BEAM'
_em_imaging.mode	'BRIGHT FIELD'
_em_imaging.nominal_cs	2.7
_em_imaging.nominal_defocus_min	800
_em_imaging.nominal_defocus_max	2500
_em_imaging.nominal_magnification	105000
_em_imaging.electron_source	'FIELD EMISSION GUN'
_em_imaging.specimen_id	1
_em_imaging.cryogen	NITROGEN

PDBx/mmCIF category	Legacy PDB format records	Description
_em_image_scans	REMARK 245	Details of the image scanning device (microdensitometer) and parameters for digitization of the image.

Example:

_em_image_scans.entry_id	1DYL
_em_image_scans.id	2
_em_image_scans.number_digital_images	48

PDBx/mmCIF category	Legacy PDB format records	Description
_em_tomography	N/A	Microscopy parameters only relevant for tomography.

Example:

_em_tomography.id	1
_em_tomography.imaging_id	1
_em_tomography.dual_tilt_axis_rotation	90.0
_em_tomography.axis1_angle_increment	2
_em_tomography.axis1_min_angle	-70.00
_em_tomography.axis1_max_angle	70.0
_em_tomography.axis2_angle_increment	2
_em_tomography.axis2_min_angle	-70.0
_em_tomography.axis2_max_angle	70.0

PDBx/mmCIF category	Legacy PDB format records	Description
_em_imaging_optics	N/A	Description of a few specialist optics apparatus.

Example:

_em_imaging_optics.id	1
_em_imaging_optics.imaging_id	1
_em_imaging_optics.chr_aberration_corrector	'CEOS manufactured Cc corrector'
_em_imaging_optics.energyfilter_lower	0
_em_imaging_optics.energyfilter_upper	15
_em_imaging_optics.energyfilter_name	FEI
_em_imaging_optics.phase_plate	?
_em_imaging_optics.sph_aberration_corrector	?

PDBx/mmCIF category	Legacy PDB format records	Description
_em_focused_ion_beam	N/A	Description of sectioning by focused_ion_beam.

Example:

No example available

PDBx/mmCIF category	Legacy PDB format records	Description
_em_image_recording	REMARK 245	Details of the image recording (either film/microdensitometer or electronic densitometer) and parameters for image digitization.

Example:

_em_image_recording.average_exposure_time	?
_em_image_recording.avg_electron_dose_per_subtomogram	?
_em_image_recording.avg_electron_dose_per_image	67
_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	?

Reconstruction

PDBx/mmCIF category	Legacy PDB format records	Description
_em_3d_reconstruction	REMARK 3 REMARK 245	Details of the 3D reconstruction procedure from 2D projections.

Example:

_em_3d_reconstruction.entry_id	8FNE
_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	3.9
_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	29303
_em_3d_reconstruction.euler_angles_details	?
_em_3d_reconstruction.num_class_averages	?
_em_3d_reconstruction.refinement_type	?
_em_3d_reconstruction.image_processing_id	1
_em_3d_reconstruction.symmetry_type	POINT

PDBx/mmCIF category	Legacy PDB format records	Description
_em_particle_selection	N/A	Details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs.

Example:

_em_particle_selection.id	1
_em_particle_selection.image_processing_id	1
_em_particle_selection.num_particles_selected	5267
_em_particle_selection.method	'INTERACTIVE'
_em_particle_selection.details	?

PDBx/mmCIF category	Legacy PDB format records	Description
_em_image_processing	N/A	Details of the EM image processing procedure.

Example:

_em_image_processing.id	1
_em_image_processing.image_recording_id	1
_em_image_processing.details	'The selected images were high-pass filtered and normalized'

PDBx/mmCIF category	Legacy PDB format records	Description
_em_ctf_correction	N/A	Description of the Contrast Transfer Function (CTF) correction.

Example:

_em_ctf_correction.details	?
_em_ctf_correction.id	1
_em_ctf_correction.em_image_processing_id	1
_em_ctf_correction.type	'PHASE FLIPPING ONLY'

Symmetry

PDBx/mmCIF category	Legacy PDB format records	Description
_em_helical_entity	N/A	Details for a helical or filament type of assembly component.

Example:

_em_helical_entity.id	1
_em_helical_entity.image_processing_id	1
_em_helical_entity.details	?
_em_helical_entity.axial_symmetry	C2
_em_helical_entity.angular_rotation_per_subunit	-0.782
_em_helical_entity.axial_rise_per_subunit	4.763

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_helical_symmetry	N/A	Details about the helical symmetry group associated with this entry.

Example:

_pdbx_helical_symmetry.entry_id	'1ABC'
_pdbx_helical_symmetry.number_of_operations	35
_pdbx_helical_symmetry.rotation_per_n_subunits	131.84
_pdbx_helical_symmetry.rise_per_n_subunits	6.10
_pdbx_helical_symmetry.n_subunits_divisor	1
_pdbx_helical_symmetry.dyad_axis	no
_pdbx_helical_symmetry.circular_symmetry	1

PDBx/mmCIF category	Legacy PDB format records	Description
_em_single_particle_entity	N/A	Details of the enforced symmetry for a single particle entity type.

Example:

_em_single_particle_entity.entry_id	8GA0
_em_single_particle_entity.id	1
_em_single_particle_entity.image_processing_id	1
_em_single_particle_entity.point_symmetry	C1

Fitting

PDBx/mmCIF category	Legacy PDB format records	Description
_em_3d_fitting	REMARK 3	Details of the method of fitting atomic coordinates from a coordinate file into a 3d-em volume map file.

Example:

_em_3d_fitting.id	1
_em_3d_fitting.entry_id	8FNE
_em_3d_fitting.method	?
_em_3d_fitting.target_criteria	?
_em_3d_fitting.details	'The initial model was generated using AlphaFold based on sequence alone.'
_em_3d_fitting.overall_b_value	?
_em_3d_fitting.ref_space	?
_em_3d_fitting.ref_protocol	'FLEXIBLE FIT'

PDBx/mmCIF category	Legacy PDB format records	Description
_em_3d_fitting_list	N/A	Details of the initial model used in fitting.

Example:

_em_3d_fitting_list.id	1
_em_3d_fitting_list.3d_fitting_id	1
_em_3d_fitting_list.pdb_entry_id	?
_em_3d_fitting_list.pdb_chain_id	?
_em_3d_fitting_list.pdb_chain_residue_range	?
_em_3d_fitting_list.details	?
_em_3d_fitting_list.chain_id	?
_em_3d_fitting_list.chain_residue_range	?
_em_3d_fitting_list.source_name	AlphaFold
_em_3d_fitting_list.type	'in silico model'
_em_3d_fitting_list.accession_code	?

Software

PDBx/mmCIF category	Legacy PDB format records	Description
_em_software	REMARK 3	Details of the software that was used for data collection, data processing, data analysis, structure calculations and refinement.

Example:

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	?	?	cryoSPARC	v2.15.0
'PARTICLE SELECTION'	?	2	1	?	?	cryoSPARC	v3.3.1
'PARTICLE SELECTION'	?	3	1	?	?	?	?
'IMAGE ACQUISITION'	?	4	?	?	1	SerialEM	v.3.6-v.3.8
MASKING	?	5	?	?	?	?	?
'CTF CORRECTION'	?	6	1	?	?	?	?
'LAYERLINE INDEXING'	?	7	1	?	?	?	?
'DIFFRACTION INDEXING'	?	8	1	?	?	?	?
'MODEL FITTING'	RosettaRelax	9	?	1	?	Rosetta	?
'MODEL FITTING'	?	10	?	1	?	'UCSF ChimeraX'	?
'MODEL FITTING'	?	11	?	1	?	'UCSF Chimera'	?
OTHER	?	12	?	?	?	?	?
'IMAGE ACQUISITION'	?	13	?	?	?	?	?
'MODEL REFINEMENT'	RosettaRefine	14	?	1	?	Rosetta	?
'MODEL REFINEMENT'	?	15	?	1	?	ISOLDE	1.2.1
'INITIAL EULER ASSIGNMENT'	'Ab-Initio Reconstruction'	16	1	?	?	cryoSPARC	v2.15.0
'INITIAL EULER ASSIGNMENT'	?	17	1	?	?	?	?
'FINAL EULER ASSIGNMENT'	?	18	1	?	?	cisTEM	1.0.0-beta
'FINAL EULER ASSIGNMENT'	?	19	1	?	?	?	?
CLASSIFICATION	?	20	1	?	?	cisTEM	1.0.0-beta
CLASSIFICATION	?	21	1	?	?	?	?
RECONSTRUCTION	?	22	1	?	?	?	?