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- EMDB-9031: Cryo-EM structure of Woodchuck hepatitis virus capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-9031
TitleCryo-EM structure of Woodchuck hepatitis virus capsid
Map data
SampleWoodchuck hepatitis virus:
virus / External core antigen
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / evasion or tolerance by virus of host immune response / viral penetration into host nucleus / viral entry into host cell / host cell cytoplasm / pathogenesis / host cell nucleus / structural molecule activity / RNA binding ...microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / evasion or tolerance by virus of host immune response / viral penetration into host nucleus / viral entry into host cell / host cell cytoplasm / pathogenesis / host cell nucleus / structural molecule activity / RNA binding / DNA binding / extracellular region
Hepatitis core antigen / Hepatitis core protein, putative zinc finger / Hepatitis core antigen / Hepatitis B virus, capsid N-terminal / Viral capsid core domain supefamily, Hepatitis B virus
External core antigen
SourceWoodchuck hepatitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.52 Å
AuthorsZhao Z / Wang JC / Zlotnick A
CitationJournal: To Be Published
Title: Crystal structure of WHV core protein mutant Y132A dimer
Authors: Zhao Z / Wang J / Zlotnick A
Validation ReportPDB-ID: 6edj

SummaryFull reportAbout validation report
DateDeposition: Aug 9, 2018 / Header (metadata) release: Sep 5, 2018 / Map release: May 1, 2019 / Update: May 1, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0314
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0314
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6edj
  • Surface level: 0.0314
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6edj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9031.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 300 pix.
= 516. Å
1.72 Å/pix.
x 300 pix.
= 516. Å
1.72 Å/pix.
x 300 pix.
= 516. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density
Contour LevelBy AUTHOR: 0.0314 / Movie #1: 0.0314
Minimum - Maximum-0.073127106 - 0.100521594
Average (Standard dev.)0.00039009104 (±0.0061770887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 516.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.721.721.72
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z516.000516.000516.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0730.1010.000

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Supplemental data

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Mask #1

Fileemd_9031_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Woodchuck hepatitis virus

EntireName: Woodchuck hepatitis virus / Number of components: 2

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Component #1: virus, Woodchuck hepatitis virus

VirusName: Woodchuck hepatitis virus / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Woodchuck hepatitis virus
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, External core antigen

ProteinName: External core antigen / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 17.126465 kDa
SourceSpecies: Woodchuck hepatitis virus
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 10 mg/mL / pH: 7.5
Support filmunspecified
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 7911
3D reconstructionSoftware: RELION / Resolution: 4.52 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 6ECS
Output model

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