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- PDB-6yng: MicroED structure of granulin determined from five native nanocry... -

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Basic information

Entry
Database: PDB / ID: 6yng
TitleMicroED structure of granulin determined from five native nanocrystalline granulovirus occlusion bodies
ComponentsGranulin
KeywordsVIRAL PROTEIN / MicroED / nanocrystalography / native crystals
Function / homologyPolyhedrin / Polyhedrin / viral occlusion body / structural molecule activity / Granulin
Function and homology information
Biological speciesCydia pomonella granulosis virus
MethodELECTRON CRYSTALLOGRAPHY / single particle reconstruction / MOLECULAR REPLACEMENT / cryo EM / Resolution: 2.8 Å
AuthorsBunker, R.D.
CitationJournal: To Be Published
Title: MicroED structure of granulin determined from five native nanocrystalline granulovirus occlusion bodies
Authors: Bunker, R.D.
History
DepositionApr 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / em_diffraction_shell ...database_2 / em_diffraction_shell / em_diffraction_stats / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_diffraction_shell.phase_residual / _em_diffraction_stats.overall_phase_error / _em_diffraction_stats.overall_phase_residual / _em_diffraction_stats.r_sym / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.pdbx_method_to_determine_struct
Revision 1.2Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: Granulin


Theoretical massNumber of molelcules
Total (without water)29,3791
Polymers29,3791
Non-polymers00
Water00
1
A: Granulin
x 12


Theoretical massNumber of molelcules
Total (without water)352,54312
Polymers352,54312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area75460 Å2
ΔGint-378 kcal/mol
Surface area129380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.657, 103.657, 103.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Granulin / Matrix protein


Mass: 29378.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cydia pomonella granulosis virus (isolate Mexico/1963)
Strain: isolate Mexico/1963 / References: UniProt: P87577

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cydia pomonella granulosis virus (isolate Mexican) / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Cydia pomonella granulosis virus (isolate Mexican)
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Cydia pomonella
Buffer solutionpH: 7.4
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
EM embeddingDetails: Undiluted sample was applied to glow-discharged 200 mesh copper Quantifoil.
Material: Ice
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: NITROGEN / Humidity: 100 % / Chamber temperature: 277 K / Details: 3 s blot, 0.5 s draining

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Data collection

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / C2 aperture diameter: 20 µm
Image recordingAverage exposure time: 2 sec. / Electron dose: 1 e/Å2 / Film or detector model: FEI CETA (4k x 4k) / Num. of diffraction images: 93 / Num. of grids imaged: 1 / Num. of real images: 93
Details: DIFFRACTON IMAGE RECORDED USING ROTATION METHOD DELPHI PHI 0.5
EM diffractionCamera length: 3600 mm
EM diffraction shellResolution: 2.8→30 Å / Fourier space coverage: 87.1 % / Multiplicity: 5 / Num. of structure factors: 4138 / Phase residual: 17.75 °
EM diffraction statsDetails: 3D ELECTRON DIFFRACTION. RESOLUTION OF MERGED DATASET DEFINED BY AN INSCRIBED CIRCLE ON THE CAMERA SURFACE, WAS LIMITED TO 3.25 A BY THE CAMERA TO SAMPLE DISTANCE.
Fourier space coverage: 87.1 % / High resolution: 2.8 Å / Num. of intensities measured: 20528 / Num. of structure factors: 4138 / Phase error rejection criteria: NULL / Rmerge: 0.321

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Processing

SoftwareName: PHENIX / Version: (dev_3313: ???) / Classification: refinement
EM software
IDNameCategory
1EPUimage acquisition
6Cootmodel fitting
8PHENIXmodel refinement
Image processingDetails: DEVELOPMENT VERSION OF THE CETA-D CAMERA
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 103.66 Å / B: 103.66 Å / C: 103.66 Å / Space group name: I23 / Space group num: 197
CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Details: RESOLUTION OF MERGED DATASET DEFINED BY AN INSCRIBED CIRCLE ON THE CAMERA SURFACE, WAS LIMITED 3.0 TO BY THE CAMERA TO SAMPLE DISTANCE. DATA INTEGRATED WITH DIALS, COMBINED WITH POINTLESS, ...Details: RESOLUTION OF MERGED DATASET DEFINED BY AN INSCRIBED CIRCLE ON THE CAMERA SURFACE, WAS LIMITED 3.0 TO BY THE CAMERA TO SAMPLE DISTANCE. DATA INTEGRATED WITH DIALS, COMBINED WITH POINTLESS, AND SCALED WITH AIMLESS. INTENSITIES CONVERTED TO STRUCTURE FACTOR AMPLITUDES WITH STARANISO. INITIAL PHASES DETERMINED BY RIGID BODY FITTING A MODEL DERIVED FROM PDB ENTRY 5G0Z IN PHENIX.REFINE. FINAL REFINEMENT CARRIED OUT IN PHENIX.REFINE
Symmetry type: 3D CRYSTAL
Atomic model buildingSpace: RECIPROCAL
Atomic model buildingPDB-ID: 5G0Z

5g0z


Accession code: 5G0Z / Source name: PDB / Type: experimental model
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G0Z

5g0z


Resolution: 2.8→2.8 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.75
RfactorNum. reflection% reflectionSelection details
Rfree0.226 400 9.99 %Random selection
Rwork0.1845 ---
obs0.1883 4004 88 %-
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.4 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0042109
ELECTRON CRYSTALLOGRAPHYf_angle_d0.832865
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d11.6551264
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.05300
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.005374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8338-3.24340.29681090.2823912ELECTRON CRYSTALLOGRAPHY68
3.2434-4.08470.2321530.1971312ELECTRON CRYSTALLOGRAPHY98
4.0847-29.92480.19291380.14951380ELECTRON CRYSTALLOGRAPHY98

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