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- EMDB-9366: Atomic structures and deletion mutant reveal different capsid-bin... -

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Basic information

Entry
Database: EMDB / ID: 9366
TitleAtomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development
Map data3D reconstruction for MCMV capsid associated with pM32 tegument protein. Contour level=4.0 was estimated while showing the map using step=2 in Chimera.
SampleMurid herpesvirus 1 (strain Smith):
virus / Major capsid protein / Tegument protein / Small capsomere-interacting protein / Minor capsid protein / Triplex capsid protein 2
Function / homologyHerpesvirus major capsid protein, upper domain superfamily / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpes virus major capsid protein / Herpesvirus VP23 like capsid protein / Small capsid protein, Herpesviridae / Herpesvirus UL11/UL32 / Herpesvirus capsid protein 2 / Small capsid protein of Herpesviridae / Herpesvirus major capsid protein ...Herpesvirus major capsid protein, upper domain superfamily / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpes virus major capsid protein / Herpesvirus VP23 like capsid protein / Small capsid protein, Herpesviridae / Herpesvirus UL11/UL32 / Herpesvirus capsid protein 2 / Small capsid protein of Herpesviridae / Herpesvirus major capsid protein / Herpesvirus large structural phosphoprotein UL32 / T=16 icosahedral viral capsid / viral capsid assembly / viral capsid / host cell nucleus / viral process / structural molecule activity / DNA binding / Major capsid protein / Tegument protein / Minor capsid protein / Small capsomere-interacting protein / Triplex capsid protein 2
Function and homology information
SourceMurid herpesvirus 1 (strain Smith) / MuHV-1 (virus)
Methodsingle particle reconstruction / cryo EM / 5 Å resolution
AuthorsLiu W / Dai XH / Jih J / Chan K / Trang P / Yu XK / Balogun R / Mei Y / Liu FY / Zhou ZH
CitationJournal: PLoS Pathog. / Year: 2019
Title: Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development.
Authors: Wei Liu / Xinghong Dai / Jonathan Jih / Karen Chan / Phong Trang / Xuekui Yu / Rilwan Balogun / Ye Mei / Fenyong Liu / Z Hong Zhou
Validation ReportPDB-ID: 6nhj

SummaryFull reportAbout validation report
DateDeposition: Dec 22, 2018 / Header (metadata) release: Mar 6, 2019 / Map release: Mar 6, 2019 / Last update: Mar 6, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6nhj
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6nhj
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9366.map.gz (map file in CCP4 format, 8388609 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1280 pix
1.35 Å/pix.
= 1729.28 Å
1280 pix
1.35 Å/pix.
= 1729.28 Å
1280 pix
1.35 Å/pix.
= 1729.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.351 Å
Density
Contour Level:4.0 (by author), 4 (movie #1):
Minimum - Maximum-7.3179355 - 13.18449
Average (Standard dev.)0.000065141685 (0.99999726)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128012801280
Origin-639.0-639.0-639.0
Limit640.0640.0640.0
Spacing128012801280
CellA=B=C: 1729.2799 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3511.3511.351
M x/y/z128012801280
origin x/y/z0.0000.0000.000
length x/y/z1729.2801729.2801729.280
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-639-639-639
NC/NR/NS128012801280
D min/max/mean-7.31813.1840.000

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Supplemental data

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Sample components

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Entire Murid herpesvirus 1 (strain Smith)

EntireName: Murid herpesvirus 1 (strain Smith) / Number of components: 6

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Component #1: virus, Murid herpesvirus 1 (strain Smith)

VirusName: Murid herpesvirus 1 (strain Smith) / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Murid herpesvirus 1 (strain Smith)

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Component #2: protein, Major capsid protein

ProteinName: Major capsid protein / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 151.673031 kDa
SourceSpecies: MuHV-1 (virus) / Strain: Smith

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Component #3: protein, Tegument protein

ProteinName: Tegument protein / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 78.749961 kDa
SourceSpecies: MuHV-1 (virus) / Strain: Smith

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Component #4: protein, Small capsomere-interacting protein

ProteinName: Small capsomere-interacting protein / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 9.845198 kDa
SourceSpecies: MuHV-1 (virus) / Strain: Smith

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Component #5: protein, Minor capsid protein

ProteinName: Minor capsid protein / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 33.281289 kDa
SourceSpecies: MuHV-1 (virus) / Strain: Smith

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Component #6: protein, Triplex capsid protein 2

ProteinName: Triplex capsid protein 2 / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 34.660262 kDa
SourceSpecies: MuHV-1 (virus) / Strain: Smith

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: PBS buffer, PH=7.4 / pH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: The grids were manually plunged into the Ethane..

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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: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 47000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: AGFA SCIENTA FILM

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Image acquisition

Image acquisitionNumber of digital images: 2200 / Scanner: NIKON SUPER COOLSCAN 9000

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 47982
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL / Overall bvalue: 2
Output model

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