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- PDB-6s2o: Granulovirus occlusion bodies by serial electron diffraction -

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Basic information

Entry
Database: PDB / ID: 6s2o
TitleGranulovirus occlusion bodies by serial electron diffraction
ComponentsGranulin
KeywordsVIRAL PROTEIN / granulovirus / occlusion body / serial crystallography
Function / homologyPolyhedrin / Polyhedrin / viral occlusion body / structural molecule activity / Granulin
Function and homology information
Biological speciesCydia pomonella granulosis virus
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.6 Å
AuthorsBuecker, R. / Mehrabi, P. / Schulz, E.C. / Hogan-Lamarre, P.
CitationJournal: Nat Commun / Year: 2020
Title: Serial protein crystallography in an electron microscope.
Authors: Robert Bücker / Pascal Hogan-Lamarre / Pedram Mehrabi / Eike C Schulz / Lindsey A Bultema / Yaroslav Gevorkov / Wolfgang Brehm / Oleksandr Yefanov / Dominik Oberthür / Günther H Kassier / ...Authors: Robert Bücker / Pascal Hogan-Lamarre / Pedram Mehrabi / Eike C Schulz / Lindsey A Bultema / Yaroslav Gevorkov / Wolfgang Brehm / Oleksandr Yefanov / Dominik Oberthür / Günther H Kassier / R J Dwayne Miller /
Abstract: Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample ...Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample delivery techniques are required. On the other hand, rotation electron diffraction (MicroED) has shown great potential as an alternative means for protein nano-crystallography. Here, we present a method for serial electron diffraction of protein nanocrystals combining the benefits of both approaches. In a scanning transmission electron microscope, crystals randomly dispersed on a sample grid are automatically mapped, and a diffraction pattern at fixed orientation is recorded from each at a high acquisition rate. Dose fractionation ensures minimal radiation damage effects. We demonstrate the method by solving the structure of granulovirus occlusion bodies and lysozyme to resolutions of 1.55 Å and 1.80 Å, respectively. Our method promises to provide rapid structure determination for many classes of materials with minimal sample consumption, using readily available instrumentation.
History
DepositionJun 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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
Water1,62190
1
A: Granulin
x 12


Theoretical massNumber of molelcules
Total (without water)352,54312
Polymers352,54312
Non-polymers00
Water21612
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 area74910 Å2
ΔGint-442 kcal/mol
Surface area126610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.200, 103.200, 103.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223

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Components

#1: Protein Granulin / / Matrix protein


Mass: 29378.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cydia pomonella granulosis virus (isolate Mexico/1963)
Strain: isolate Mexico/1963
Production host: Cydia pomonella granulosis virus (isolate Mexican)
References: UniProt: P87577
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Cydia pomonella granulosis virus (isolate Mexican) / Type: VIRUS / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Cydia pomonella granulosis virus (isolate Mexican)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION / C2 aperture diameter: 5 µm / Alignment procedure: OTHER
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Temperature (max): 100 K / Temperature (min): 93 K
Image recordingAverage exposure time: 0.01 sec. / Electron dose: 4.7 e/Å2 / Film or detector model: OTHER / Num. of diffraction images: 32000 / Num. of grids imaged: 1
Image scansSampling size: 50 µm / Width: 1536 / Height: 512
EM diffractionCamera length: 2580 mm / Tilt angle list: 0
EM diffraction shellResolution: 10→1.55 Å / Fourier space coverage: 1 % / Multiplicity: 1 / Num. of structure factors: 1 / Phase residual: 1 °
EM diffraction statsFourier space coverage: 100 % / High resolution: 1.6 Å / Num. of intensities measured: 9650574 / Num. of structure factors: 23422 / Phase error: 13.64 ° / Phase residual: 1 ° / Phase error rejection criteria: 0 / Rmerge: 0.093 / Rsym: 0.093
ReflectionBiso Wilson estimate: 16.07 Å2

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Processing

Software
NameVersionClassification
phenix.refine1.17_3644refinement
PHENIX1.17_3644refinement
EM software
IDNameVersionCategory
6Coot0.8.9.2model fitting
8PHENIX1.17molecular replacement
12Coot3D reconstruction
13PHENIX1.17model refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 103.2 Å / B: 103.2 Å / C: 103.2 Å / Space group name: I23 / Space group num: 197
CTF correctionDetails: Data reduction and structure solution using X-ray crystallography codes (CrystFEL, Phaser, cctbx.xfel, Coot)
Type: NONE
3D reconstructionResolution: 1.6 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingPDB-ID: 5G0Z

5g0z


Pdb chain-ID: A / Pdb chain residue range: 6-248
RefinementResolution: 1.55→72.97 Å / SU ML: 0.1976 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.1215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1965 1297 4.87 %
Rwork0.1705 25338 -
obs0.1718 26635 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.29 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.01162099
ELECTRON CRYSTALLOGRAPHYf_angle_d1.13132854
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0767300
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0072373
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d6.1208278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.610.36011610.32422770ELECTRON CRYSTALLOGRAPHY99.59
1.61-1.690.30841380.28442783ELECTRON CRYSTALLOGRAPHY99.97
1.69-1.770.28321340.23652800ELECTRON CRYSTALLOGRAPHY100
1.77-1.890.2741630.21342770ELECTRON CRYSTALLOGRAPHY100
1.89-2.030.20511740.17542790ELECTRON CRYSTALLOGRAPHY100
2.03-2.240.22061170.16612817ELECTRON CRYSTALLOGRAPHY99.97
2.24-2.560.19081190.16962844ELECTRON CRYSTALLOGRAPHY100
2.56-3.220.18831290.15562858ELECTRON CRYSTALLOGRAPHY100
3.23-72.970.13831620.12822906ELECTRON CRYSTALLOGRAPHY100

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