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- PDB-8hey: One CVSC-binding penton vertex in HCMV B-capsid -

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Basic information

Entry
Database: PDB / ID: 8hey
TitleOne CVSC-binding penton vertex in HCMV B-capsid
Components
  • (Capsid vertex component ...) x 2
  • (Triplex capsid protein ...) x 2
  • Major capsid protein
  • Small capsomere-interacting protein
KeywordsVIRAL PROTEIN / B-capsid / one CVSC-binding penton vertex / asymmetric reconstruction / VIRUS
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral genome packaging / viral capsid assembly / viral release from host cell / chromosome organization / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Small capsid protein, Herpesviridae / Small capsid protein of Herpesviridae / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus UL25 / Herpesvirus UL25 family / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid protein 2 / Herpesvirus VP23 like capsid protein ...Small capsid protein, Herpesviridae / Small capsid protein of Herpesviridae / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus UL25 / Herpesvirus UL25 family / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid protein 2 / Herpesvirus VP23 like capsid protein / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein
Similarity search - Domain/homology
Major capsid protein / UL77 protein / Capsid vertex component 1 / Small capsomere-interacting protein / Capsid triplex subunit 2 / Capsid triplex subunit 1
Similarity search - Component
Biological speciesHuman betaherpesvirus 5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLi, Z. / Yu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900869 China
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-electron microscopy structures of capsids and in situ portals of DNA-devoid capsids of human cytomegalovirus.
Authors: Zhihai Li / Jingjing Pang / Rongchao Gao / Qingxia Wang / Maoyan Zhang / Xuekui Yu /
Abstract: The portal-scaffold complex is believed to nucleate the assembly of herpesvirus procapsids. During capsid maturation, two events occur: scaffold expulsion and DNA incorporation. The portal-scaffold ...The portal-scaffold complex is believed to nucleate the assembly of herpesvirus procapsids. During capsid maturation, two events occur: scaffold expulsion and DNA incorporation. The portal-scaffold interaction and the conformational changes that occur to the portal during the different stages of capsid formation have yet to be elucidated structurally. Here we present high-resolution structures of the A- and B-capsids and in-situ portals of human cytomegalovirus. We show that scaffolds bind to the hydrophobic cavities formed by the dimerization and Johnson-fold domains of the major capsid proteins. We further show that 12 loop-helix-loop fragments-presumably from the scaffold domain-insert into the hydrophobic pocket of the portal crown domain. The portal also undergoes significant changes both positionally and conformationally as it accompanies DNA packaging. These findings unravel the mechanism by which the portal interacts with the scaffold to nucleate capsid assembly and further our understanding of scaffold expulsion and DNA incorporation.
History
DepositionNov 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: Small capsomere-interacting protein
i: Small capsomere-interacting protein
j: Small capsomere-interacting protein
a: Major capsid protein
D: Major capsid protein
Y: Major capsid protein
Z: Major capsid protein
h: Triplex capsid protein 2
I: Triplex capsid protein 2
n: Triplex capsid protein 2
o: Triplex capsid protein 2
g: Triplex capsid protein 1
m: Triplex capsid protein 1
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
M: Capsid vertex component 1
N: Capsid vertex component 2
O: Capsid vertex component 2


Theoretical massNumber of molelcules
Total (without water)1,545,11022
Polymers1,545,11022
Non-polymers00
Water00
1
T: Small capsomere-interacting protein
i: Small capsomere-interacting protein
j: Small capsomere-interacting protein
a: Major capsid protein
D: Major capsid protein
Y: Major capsid protein
Z: Major capsid protein
h: Triplex capsid protein 2
I: Triplex capsid protein 2
n: Triplex capsid protein 2
o: Triplex capsid protein 2
g: Triplex capsid protein 1
m: Triplex capsid protein 1
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
M: Capsid vertex component 1
N: Capsid vertex component 2
O: Capsid vertex component 2
x 5


  • complete point assembly
  • Evidence: microscopy
  • 7.73 MDa, 110 polymers
Theoretical massNumber of molelcules
Total (without water)7,725,549110
Polymers7,725,549110
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C5 (5 fold cyclic))

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Components

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Protein , 2 types, 13 molecules TijQRSaDYZABC

#1: Protein
Small capsomere-interacting protein


Mass: 8495.924 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 / References: UniProt: A8T7C4
#2: Protein
Major capsid protein / MCP


Mass: 154048.906 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 / References: UniProt: A0A1U8QPG3

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Triplex capsid protein ... , 2 types, 6 molecules hInogm

#3: Protein
Triplex capsid protein 2


Mass: 34635.750 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 / References: UniProt: Q6RXF2
#4: Protein Triplex capsid protein 1


Mass: 33071.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 / References: UniProt: Q6RXH2

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Capsid vertex component ... , 2 types, 3 molecules MNO

#5: Protein Capsid vertex component 1 / UL93


Mass: 68567.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 / References: UniProt: A0A6C0PJD3
#6: Protein Capsid vertex component 2 / UL77


Mass: 71269.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human betaherpesvirus 5 / References: UniProt: A0A3G6XKK5

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Human betaherpesvirus 5 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Human betaherpesvirus 5
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40903 / Symmetry type: POINT

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