6PPH

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

  • Classification: VIRAL PROTEIN
  • Organism(s): Human herpesvirus 8, Human herpesvirus 8 type P (isolate GK18)

  • 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; National Institutes of Health/National Institute of Dental and Craniofacial Research; National Institutes of Health/National Institute Of Allergy and Infectious Diseases; National Institutes of Health/National Cancer Institute; Other government; National Institutes of Health/National Center for Research Resources; National Science Foundation (United States) 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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

    California NanoSystems Institute (CNSI), University of California, Los Angeles, Los Angeles, CA 90095, USA.,Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China (USTC), Hefei, Anhui 230026, China.,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.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; 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; Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China (USTC), Hefei, Anhui 230026, China.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Molecular and Medical Pharmacology, 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: rsun@mednet.ucla.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid vertex component 1
k
454Human herpesvirus 8Mutation(s): 0 
Gene Names: ORF32 (CVC1)
Find proteins for Q76RH8 (Human herpesvirus 8)
Go to UniProtKB:  Q76RH8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Capsid vertex component 2
l, m
549Human herpesvirus 8Mutation(s): 0 
Gene Names: ORF19 (CVC2)
Find proteins for Q76RI7 (Human herpesvirus 8)
Go to UniProtKB:  Q76RI7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Large tegument protein deneddylase
n, o
2635Human herpesvirus 8 type P (isolate GK18)Mutation(s): 0 
EC: 3.4.19.12, 3.4.22.-
Find proteins for Q2HR64 (Human herpesvirus 8 type P (isolate GK18))
Go to UniProtKB:  Q2HR64
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Triplex capsid protein 1
5, b
331Human herpesvirus 8Mutation(s): 0 
Gene Names: ORF62 (TRX1)
Find proteins for Q76RF6 (Human herpesvirus 8)
Go to UniProtKB:  Q76RF6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Triplex capsid protein 2
6, 7, c, d
305Human herpesvirus 8Mutation(s): 0 
Gene Names: ORF26 (TRX2)
Find proteins for C7E5A9 (Human herpesvirus 8)
Go to UniProtKB:  C7E5A9
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Major capsid protein
4, S, T, X, W
1376Human herpesvirus 8Mutation(s): 0 
Gene Names: ORF25 (MCP)
Find proteins for D0UZN7 (Human herpesvirus 8)
Go to UniProtKB:  D0UZN7
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Small capsomere-interacting protein
A, 2, 3, 1, 0
170Human herpesvirus 8Mutation(s): 0 
Gene Names: ORF65 (SCP)
Find proteins for Q76RF4 (Human herpesvirus 8)
Go to UniProtKB:  Q76RF4
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
phenix.real_space_refinerefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM071940
National Institutes of Health/National Institute of Dental and Craniofacial ResearchUnited StatesDE025567
National Institutes of Health/National Institute of Dental and Craniofacial ResearchUnited StatesDE028583
National Institutes of Health/National Institute of Dental and Craniofacial ResearchUnited StatesDE027901
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI094386
National Institutes of Health/National Cancer InstituteUnited StatesCA177322
National Institutes of Health/National Cancer InstituteUnited StatesCA091791
National Institutes of Health/National Institute of Dental and Craniofacial ResearchUnited StatesDE023591
Other governmentChina2017YFA0505300
Other governmentChina2016YFA0400900
National Institutes of Health/National Center for Research ResourcesUnited States1S10RR23057
National Institutes of Health/National Institute of General Medical SciencesUnited States1U24GM116792
National Science Foundation (United States)United StatesDBI-1338135
National Science Foundation (United States)United StatesDMR-1548924

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-09-18
    Type: Data collection, Database references