6CGR

CryoEM structure of herpes simplex virus 1 capsid with associated tegument protein complexes.

  • Classification: VIRUS
  • Organism(s): Human herpesvirus 1

  • Deposited: 2018-02-20 Released: 2018-03-14 
  • Deposition Author(s): Dai, X.H., Zhou, Z.H.
  • Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR); National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS); National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID); National Institutes of Health/Office of the Director; National Science Foundation (NSF, United States) 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Structure of the herpes simplex virus 1 capsid with associated tegument protein complexes.

Dai, X., Zhou, Z.H.

(2018) Science 360: --

  • DOI: 10.1126/science.aao7298

  • PubMed Abstract: 

    • Herpes simplex viruses (HSVs) rely on capsid-associated tegument complex (CATC) for long-range axonal transport of their genome-containing capsids between sites of infection and neuronal cell bodies. Here we report cryo-electron microscopy structures ...

    Herpes simplex viruses (HSVs) rely on capsid-associated tegument complex (CATC) for long-range axonal transport of their genome-containing capsids between sites of infection and neuronal cell bodies. Here we report cryo-electron microscopy structures of the HSV-1 capsid with CATC up to 3.5-angstrom resolution and atomic models of multiple conformers of capsid proteins VP5, VP19c, VP23, and VP26 and tegument proteins pUL17, pUL25, and pUL36. Crowning every capsid vertex are five copies of heteropentameric CATC, each containing a pUL17 monomer supporting the coiled-coil helix bundle of a pUL25 dimer and a pUL36 dimer, thus positioning their flexible domains for potential involvement in nuclear capsid egress and axonal capsid transport. Notwithstanding newly discovered fold conservation between triplex proteins and bacteriophage λ protein gpD and the previously recognized bacteriophage HK97 gp5-like fold in VP5, HSV-1 capsid proteins exhibit extraordinary diversity in forms of domain insertion and conformational polymorphism, not only for interactions with tegument proteins but also for encapsulation of large genomes.

    Organizational Affiliation: 

    Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA. hong.zhou@ucla.edu.,Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major capsid protein
A, B, C, D, E, F, M, N, O, S, T, U, V, W, X, 4
1374Human herpesvirus 1Mutation(s): 0 
Gene Names: UL19 (MCP)
Find proteins for G8HBD2 (Human herpesvirus 1)
Go to UniProtKB:  G8HBD2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small capsomere-interacting protein
G, H, I, J, K, L, P, Q, R, Y, Z, 0, 1, 2, 3
112Human herpesvirus 1Mutation(s): 0 
Gene Names: UL35 (SCP)
Find proteins for Q25BW6 (Human herpesvirus 1)
Go to UniProtKB:  Q25BW6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Triplex capsid protein 1
5, 8, b, e, h
465Human herpesvirus 1Mutation(s): 0 
Gene Names: UL38 (TRX1)
Find proteins for F8REX2 (Human herpesvirus 1)
Go to UniProtKB:  F8REX2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Triplex capsid protein 2
6, 7, 9, a, c, d, f, g, i, j
318Human herpesvirus 1Mutation(s): 0 
Gene Names: UL18 (TRX2)
Find proteins for G8H8D9 (Human herpesvirus 1)
Go to UniProtKB:  G8H8D9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Capsid vertex component 1
k
703Human herpesvirus 1Mutation(s): 0 
Gene Names: UL17 (CVC1)
Find proteins for F8RFA1 (Human herpesvirus 1)
Go to UniProtKB:  F8RFA1
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Capsid vertex component 2
l, m
580Human herpesvirus 1Mutation(s): 0 
Gene Names: UL25 (CVC2)
Find proteins for G8HBD8 (Human herpesvirus 1)
Go to UniProtKB:  G8HBD8
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Large tegument protein deneddylase
n, o
3139Human herpesvirus 1Mutation(s): 0 
Gene Names: UL36
EC: 3.4.19.12, 3.4.22.-
Find proteins for G8HBF0 (Human herpesvirus 1)
Go to UniProtKB:  G8HBF0
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-02-20 
  • Released Date: 2018-03-14 
  • Deposition Author(s): Dai, X.H., Zhou, Z.H.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesDE025567
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM071940
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI094386
National Institutes of Health/Office of the DirectorUnited States1S10OD018111
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1U24GM116792
National Science Foundation (NSF, United States)United StatesDBI-1338135

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Data collection, Database references
  • Version 1.2: 2018-04-11
    Type: Advisory, Data collection
  • Version 1.3: 2018-04-18
    Type: Data collection, Database references
  • Version 1.4: 2019-11-27
    Type: Author supporting evidence