6PPH

Kaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex register, CATC-binding structure

  • Classification: VIRAL PROTEIN
  • Organism(s): Human herpesvirus 8 strain GK18
  • Mutation(s): No 

  • Deposited: 2019-07-06 Released: 2019-09-11 
  • Deposition Author(s): Gong, D., Dai, X., Jih, J., Liu, Y.T., Bi, G.Q., Sun, R., Zhou, Z.H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI), Other government, National Institutes of Health/National Center for Research Resources (NIH/NCRR), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DNA-Packing Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus KSHV.

Gong, D.Dai, X.Jih, J.Liu, Y.T.Bi, G.Q.Sun, R.Zhou, Z.H.

(2019) Cell 178: 1329-1343.e12

  • DOI: 10.1016/j.cell.2019.07.035
  • Primary Citation of Related Structures:  
    6PPI, 6PPH, 6PPB, 6PPD

  • PubMed Abstract: 
  • Assembly of Kaposi's sarcoma-associated herpesvirus (KSHV) begins at a bacteriophage-like portal complex that nucleates formation of an icosahedral capsid with capsid-associated tegument complexes (CATCs) and facilitates translocation of an ∼150-kb d ...

    Assembly of Kaposi's sarcoma-associated herpesvirus (KSHV) begins at a bacteriophage-like portal complex that nucleates formation of an icosahedral capsid with capsid-associated tegument complexes (CATCs) and facilitates translocation of an ∼150-kb dsDNA genome, followed by acquisition of a pleomorphic tegument and envelope. Because of deviation from icosahedral symmetry, KSHV portal and tegument structures have largely been obscured in previous studies. Using symmetry-relaxed cryo-EM, we determined the in situ structure of the KSHV portal and its interactions with surrounding capsid proteins, CATCs, and the terminal end of KSHV's dsDNA genome. Our atomic models of the portal and capsid/CATC, together with visualization of CATCs' variable occupancy and alternate orientation of CATC-interacting vertex triplexes, suggest a mechanism whereby the portal orchestrates procapsid formation and asymmetric long-range determination of CATC attachment during DNA packaging prior to pleomorphic tegumentation/envelopment. Structure-based mutageneses confirm that a triplex deep binding groove for CATCs is a hotspot that holds promise for antiviral development.


    Organizational Affiliation

    Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute (CNSI), University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: hong.zhou@ucla.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid vertex component 1k454Human herpesvirus 8 strain GK18Mutation(s): 0 
Gene Names: CVC1ORF32
Find proteins for F5HB39 (Human herpesvirus 8 type P (isolate GK18))
Explore F5HB39 
Go to UniProtKB:  F5HB39
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid vertex component 2lm549Human herpesvirus 8 strain GK18Mutation(s): 0 
Gene Names: CVC2ORF19
Find proteins for Q2HRB3 (Human herpesvirus 8 type P (isolate GK18))
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Go to UniProtKB:  Q2HRB3
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Large tegument protein deneddylaseno2635Human herpesvirus 8 strain GK18Mutation(s): 0 
Gene Names: ORF64
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
Find proteins for Q2HR64 (Human herpesvirus 8 type P (isolate GK18))
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Go to UniProtKB:  Q2HR64
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Triplex capsid protein 15b331Human herpesvirus 8 strain GK18Mutation(s): 0 
Gene Names: TRX1ORF62
Find proteins for F5H8Y5 (Human herpesvirus 8 type P (isolate GK18))
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Go to UniProtKB:  F5H8Y5
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Triplex capsid protein 267cd305Human herpesvirus 8 strain GK18Mutation(s): 0 
Find proteins for C7E5A9 (Human herpesvirus 8)
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Go to UniProtKB:  C7E5A9
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid protein4STWX1376Human herpesvirus 8 strain GK18Mutation(s): 0 
Gene Names: MCPORF25
Find proteins for Q2HRA7 (Human herpesvirus 8 type P (isolate GK18))
Explore Q2HRA7 
Go to UniProtKB:  Q2HRA7
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small capsomere-interacting protein0123A170Human herpesvirus 8 strain GK18Mutation(s): 0 
Gene Names: SCPORF65
Find proteins for Q2HR63 (Human herpesvirus 8 type P (isolate GK18))
Explore Q2HR63 
Go to UniProtKB:  Q2HR63
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM071940
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesDE025567
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesDE028583
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesDE027901
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI094386
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA177322
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA091791
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesDE023591
Other governmentChina2017YFA0505300
Other governmentChina2016YFA0400900
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States1S10RR23057
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1U24GM116792
National Science Foundation (NSF, United States)United StatesDBI-1338135
National Science Foundation (NSF, United States)United StatesDMR-1548924

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence