6B43

CryoEM structure and atomic model of the Kaposi's sarcoma-associated herpesvirus capsid

  • Classification: VIRUS
  • Organism(s): Human herpesvirus 8

  • Deposited: 2017-09-25 Released: 2017-11-08 
  • Deposition Author(s): Dai, X.H., Gong, D.Y., Sun, R., 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/National Cancer Institute (NIH/NCI); 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 1.6 of the entry. See complete history

Literature

Structure and mutagenesis reveal essential capsid protein interactions for KSHV replication.

Dai, X.Gong, D.Lim, H.Jih, J.Wu, T.T.Sun, R.Zhou, Z.H.

(2018) Nature 553: 521-525

  • DOI: 10.1038/nature25438

  • PubMed Abstract: 
  • Kaposi's sarcoma-associated herpesvirus (KSHV) causes Kaposi's sarcoma, a cancer that commonly affects patients with AIDS and which is endemic in sub-Saharan Africa. The KSHV capsid is highly pressurized by its double-stranded DNA genome, as are the ...

    Kaposi's sarcoma-associated herpesvirus (KSHV) causes Kaposi's sarcoma, a cancer that commonly affects patients with AIDS and which is endemic in sub-Saharan Africa. The KSHV capsid is highly pressurized by its double-stranded DNA genome, as are the capsids of the eight other human herpesviruses. Capsid assembly and genome packaging of herpesviruses are prone to interruption and can therefore be targeted for the structure-guided development of antiviral agents. However, herpesvirus capsids-comprising nearly 3,000 proteins and over 1,300 Å in diameter-present a formidable challenge to atomic structure determination and functional mapping of molecular interactions. Here we report a 4.2 Å resolution structure of the KSHV capsid, determined by electron-counting cryo-electron microscopy, and its atomic model, which contains 46 unique conformers of the major capsid protein (MCP), the smallest capsid protein (SCP) and the triplex proteins Tri1 and Tri2. Our structure and mutagenesis results reveal a groove in the upper domain of the MCP that contains hydrophobic residues that interact with the SCP, which in turn crosslinks with neighbouring MCPs in the same hexon to stabilize the capsid. Multiple levels of MCP-MCP interaction-including six sets of stacked hairpins lining the hexon channel, disulfide bonds across channel and buttress domains in neighbouring MCPs, and an interaction network forged by the N-lasso domain and secured by the dimerization domain-define a robust capsid that is resistant to the pressure exerted by the enclosed genome. The triplexes, each composed of two Tri2 molecules and a Tri1 molecule, anchor to the capsid floor via a Tri1 N-anchor to plug holes in the MCP network and rivet the capsid floor. These essential roles of the MCP N-lasso and Tri1 N-anchor are verified by serial-truncation mutageneses. Our proof-of-concept demonstration of the use of polypeptides that mimic the smallest capsid protein to inhibit KSHV lytic replication highlights the potential for exploiting the interaction hotspots revealed in our atomic structure to develop antiviral agents.


    Organizational Affiliation

    Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA.,The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, California 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
1376Human herpesvirus 8Mutation(s): 0 
Gene Names: ORF25 (MCP)
Find proteins for D0UZN7 (Human herpesvirus 8)
Go to UniProtKB:  D0UZN7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small capsomere-interacting protein
G, H, I, J, K, L, P, Q, R, Y, Z, 0, 1, 2, 3
170Human herpesvirus 8Mutation(s): 0 
Gene Names: ORF65 (SCP)
Find proteins for Q76RF4 (Human herpesvirus 8)
Go to UniProtKB:  Q76RF4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Triplex capsid protein 1
5, 8, b, e, h
331Human herpesvirus 8Mutation(s): 0 
Gene Names: ORF62 (TRX1)
Find proteins for Q76RF6 (Human herpesvirus 8)
Go to UniProtKB:  Q76RF6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Triplex capsid protein 2
6, 7, 9, a, c, d, f, g, i, j
305Human herpesvirus 8Mutation(s): 0 
Gene Names: ORF26 (TRX2)
Find proteins for C7E5A9 (Human herpesvirus 8)
Go to UniProtKB:  C7E5A9
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



Entry History & Funding Information

Deposition Data


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/National Cancer Institute (NIH/NCI)United StatesCA091791
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA177322
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: 2017-11-08
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Author supporting evidence, Other
  • Version 1.2: 2018-01-31
    Type: Database references
  • Version 1.3: 2018-02-07
    Type: Database references
  • Version 1.4: 2018-04-11
    Type: Advisory, Data collection
  • Version 1.5: 2019-11-27
    Type: Author supporting evidence
  • Version 1.6: 2019-12-18
    Type: Other