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- PDB-6m6h: Structure of HSV2 C-capsid portal vertex -

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Basic information

Entry
Database: PDB / ID: 6m6h
TitleStructure of HSV2 C-capsid portal vertex
Components
  • (Capsid vertex component ...) x 2
  • (Triplex capsid protein ...) x 2
  • Large tegument protein deneddylase
  • Major capsid protein
  • Small capsomere-interacting protein
KeywordsVIRAL PROTEIN / HSV2 / Portal vertex / Complex
Function / homology
Function and homology information


viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / viral DNA genome replication / viral process / chromosome organization / viral penetration into host nucleus / viral capsid ...viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / viral DNA genome replication / viral process / chromosome organization / viral penetration into host nucleus / viral capsid / host cell / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis / DNA binding
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region ...Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / 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
Capsid triplex subunit 2 / Small capsomere-interacting protein / Capsid triplex subunit 1 / Capsid vertex component 1 / Major capsid protein / Capsid vertex component 2 / Large tegument protein deneddylase
Similarity search - Component
Biological speciesHuman herpesvirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsWang, X.X. / Wang, N.
CitationJournal: Protein Cell / Year: 2020
Title: Structures of the portal vertex reveal essential protein-protein interactions for Herpesvirus assembly and maturation.
Authors: Nan Wang / Wenyuan Chen / Ling Zhu / Dongjie Zhu / Rui Feng / Jialing Wang / Bin Zhu / Xinzheng Zhang / Xiaoqing Chen / Xianjie Liu / Runbin Yan / Dongyao Ni / Grace Guoying Zhou / Hongrong ...Authors: Nan Wang / Wenyuan Chen / Ling Zhu / Dongjie Zhu / Rui Feng / Jialing Wang / Bin Zhu / Xinzheng Zhang / Xiaoqing Chen / Xianjie Liu / Runbin Yan / Dongyao Ni / Grace Guoying Zhou / Hongrong Liu / Zihe Rao / Xiangxi Wang /
History
DepositionMar 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Capsid vertex component 1
H: Capsid vertex component 2
I: Capsid vertex component 2
J: Small capsomere-interacting protein
K: Small capsomere-interacting protein
L: Small capsomere-interacting protein
M: Small capsomere-interacting protein
N: Small capsomere-interacting protein
O: Small capsomere-interacting protein
P: Large tegument protein deneddylase
Q: Large tegument protein deneddylase
R: Triplex capsid protein 2
S: Triplex capsid protein 2
T: Triplex capsid protein 1


Theoretical massNumber of molelcules
Total (without water)1,951,55620
Polymers1,951,55620
Non-polymers00
Water00
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Capsid vertex component 1
H: Capsid vertex component 2
I: Capsid vertex component 2
J: Small capsomere-interacting protein
K: Small capsomere-interacting protein
L: Small capsomere-interacting protein
M: Small capsomere-interacting protein
N: Small capsomere-interacting protein
O: Small capsomere-interacting protein
P: Large tegument protein deneddylase
Q: Large tegument protein deneddylase
R: Triplex capsid protein 2
S: Triplex capsid protein 2
T: Triplex capsid protein 1
x 5


Theoretical massNumber of molelcules
Total (without water)9,757,780100
Polymers9,757,780100
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 , 3 types, 14 molecules ABCDEFJKLMNOPQ

#1: Protein
Major capsid protein / MCP / VP5


Mass: 149399.359 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: P89442
#4: Protein
Small capsomere-interacting protein / VP26


Mass: 12147.707 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I257
#5: Protein Large tegument protein deneddylase / UL36


Mass: 330496.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2
References: UniProt: P89459, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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

#2: Protein Capsid vertex component 1 / UL17


Mass: 74811.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: P89440
#3: Protein Capsid vertex component 2 / UL25


Mass: 63604.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: P89448

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Triplex capsid protein ... , 2 types, 3 molecules RST

#6: Protein Triplex capsid protein 2 / VP23


Mass: 34373.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I239
#7: Protein Triplex capsid protein 1 / VP19


Mass: 50512.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I260

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Details

Has protein modificationY

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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 alphaherpesvirus 2 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Human alphaherpesvirus 2
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / 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: DARK FIELD
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1130FEI FALCON II (4k x 4k)
2130FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35698 / Symmetry type: POINT

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