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

  • 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 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 Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid vertex component 1A [auth k]454Human herpesvirus 8 strain GK18Mutation(s): 0 
UniProt
Find proteins for F5HB39 (Human herpesvirus 8 type P (isolate GK18))
Explore F5HB39 
Go to UniProtKB:  F5HB39
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UniProt GroupF5HB39
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid vertex component 2B [auth l],
C [auth m]
549Human herpesvirus 8 strain GK18Mutation(s): 0 
UniProt
Find proteins for Q2HRB3 (Human herpesvirus 8 type P (isolate GK18))
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UniProt GroupQ2HRB3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Large tegument protein deneddylaseD [auth n],
E [auth o]
2,635Human herpesvirus 8 strain GK18Mutation(s): 0 
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for Q2HR64 (Human herpesvirus 8 type P (isolate GK18))
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Go to UniProtKB:  Q2HR64
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UniProt GroupQ2HR64
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 1F [auth 5],
I [auth b]
331Human herpesvirus 8 strain GK18Mutation(s): 0 
UniProt
Find proteins for F5H8Y5 (Human herpesvirus 8 type P (isolate GK18))
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UniProt GroupF5H8Y5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Triplex capsid protein 2G [auth 6],
H [auth 7],
J [auth c],
K [auth d]
305Human herpesvirus 8 strain GK18Mutation(s): 0 
UniProt
Find proteins for C7E5A9 (Human herpesvirus 8)
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UniProt GroupC7E5A9
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid proteinL [auth 4],
O [auth S],
Q [auth T],
S [auth X],
U [auth W]
1,376Human herpesvirus 8 strain GK18Mutation(s): 0 
UniProt
Find proteins for Q2HRA7 (Human herpesvirus 8 type P (isolate GK18))
Explore Q2HRA7 
Go to UniProtKB:  Q2HRA7
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UniProt GroupQ2HRA7
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small capsomere-interacting proteinM [auth A],
N [auth 2],
P [auth 3],
R [auth 1],
T [auth 0]
170Human herpesvirus 8 strain GK18Mutation(s): 0 
UniProt
Find proteins for Q2HR63 (Human herpesvirus 8 type P (isolate GK18))
Explore Q2HR63 
Go to UniProtKB:  Q2HR63
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UniProt GroupQ2HR63
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.13

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  (Full details and data files)

  • 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