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- PDB-7et3: C5 portal vertex in the enveloped virion capsid -

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Basic information

Entry
Database: PDB / ID: 7et3
TitleC5 portal vertex in the enveloped virion capsid
Components
  • (Capsid vertex component ...) x 2
  • (Triplex capsid protein ...) x 2
  • Large tegument protein deneddylase
  • Major capsid protein
  • ORFL92C_UL32
  • Small capsomere-interacting protein
KeywordsVIRAL PROTEIN / C5 portal vertex / enveloped capsid
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / viral release from host cell / chromosome organization / viral process / virion component / viral capsid / symbiont-mediated perturbation of host ubiquitin-like protein modification ...T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / viral release from host cell / chromosome organization / viral process / virion component / viral capsid / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / cysteine-type deubiquitinase activity / host cell nucleus / structural molecule activity / proteolysis / DNA binding
Similarity search - Function
Herpesvirus UL11/UL32 / Herpesvirus large structural phosphoprotein UL32 / Small capsid protein, Herpesviridae / Small capsid protein of Herpesviridae / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein ...Herpesvirus UL11/UL32 / Herpesvirus large structural phosphoprotein UL32 / Small capsid protein, Herpesviridae / Small capsid protein of Herpesviridae / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / 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 / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Major capsid protein / UL77 protein / UL48 protein / Capsid vertex component 1 / ORFL92C_UL32 / Small capsomere-interacting protein / Capsid triplex subunit 2 / Capsid triplex subunit 1
Similarity search - Component
Biological speciesHuman cytomegalovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLi, Z. / Yu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900869 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for genome packaging, retention, and ejection in human cytomegalovirus.
Authors: Zhihai Li / Jingjing Pang / Lili Dong / Xuekui Yu /
Abstract: How the human cytomegalovirus (HCMV) genome-the largest among human herpesviruses-is packaged, retained, and ejected remains unclear. We present the in situ structures of the symmetry-mismatched ...How the human cytomegalovirus (HCMV) genome-the largest among human herpesviruses-is packaged, retained, and ejected remains unclear. We present the in situ structures of the symmetry-mismatched portal and the capsid vertex-specific components (CVSCs) of HCMV. The 5-fold symmetric 10-helix anchor-uncommon among known portals-contacts the portal-encircling DNA, which is presumed to squeeze the portal as the genome packaging proceeds. We surmise that the 10-helix anchor dampens this action to delay the portal reaching a "head-full" packaging state, thus facilitating the large genome to be packaged. The 6-fold symmetric turret, latched via a coiled coil to a helix from a major capsid protein, supports the portal to retain the packaged genome. CVSCs at the penton vertices-presumed to increase inner capsid pressure-display a low stoichiometry, which would aid genome retention. We also demonstrate that the portal and capsid undergo conformational changes to facilitate genome ejection after viral cell entry.
History
DepositionMay 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure viewerMolecule:
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Assembly

Deposited unit
h: Triplex capsid protein 2
I: Triplex capsid protein 2
H: Large tegument protein deneddylase
P: Large tegument protein deneddylase
n: Triplex capsid protein 2
o: Triplex capsid protein 2
g: Triplex capsid protein 1
m: Triplex capsid protein 1
M: Capsid vertex component 1
N: Capsid vertex component 2
O: Capsid vertex component 2
1: ORFL92C_UL32
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
T: Small capsomere-interacting protein
i: Small capsomere-interacting protein
j: Small capsomere-interacting protein
a: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
Y: Major capsid protein
Z: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)2,002,47623
Polymers2,002,47623
Non-polymers00
Water00
1
h: Triplex capsid protein 2
I: Triplex capsid protein 2
H: Large tegument protein deneddylase
P: Large tegument protein deneddylase
n: Triplex capsid protein 2
o: Triplex capsid protein 2
g: Triplex capsid protein 1
m: Triplex capsid protein 1
M: Capsid vertex component 1
N: Capsid vertex component 2
O: Capsid vertex component 2
1: ORFL92C_UL32
R: Small capsomere-interacting protein
S: Small capsomere-interacting protein
T: Small capsomere-interacting protein
i: Small capsomere-interacting protein
j: Small capsomere-interacting protein
a: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
Y: Major capsid protein
Z: Major capsid protein
x 5


Theoretical massNumber of molelcules
Total (without water)10,012,382115
Polymers10,012,382115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
2


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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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Triplex capsid protein ... , 2 types, 6 molecules hInogm

#1: Protein
Triplex capsid protein 2


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


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

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Protein , 4 types, 14 molecules HP1RSTijaBCDYZ

#2: Protein Large tegument protein deneddylase / UL48


Mass: 253541.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus
References: UniProt: A0A3G6XL22, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#6: Protein ORFL92C_UL32


Mass: 112829.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus / References: UniProt: A0A6C0PKC1
#7: Protein
Small capsomere-interacting protein


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


Mass: 154048.906 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus / References: UniProt: A0A1U8QPG3

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

#4: Protein Capsid vertex component 1 / UL93


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


Mass: 71269.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus / 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: 7.5
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
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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23136 / Symmetry type: POINT

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