7NXQ | pdb_00007nxq

Structure of the pentameric C-terminal domain of the capsid protein from Kaposi's sarcoma-associated herpesvirus (KSHV)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.235 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.207 (Depositor) 
  • R-Value Observed: 
    0.208 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7NXQ

This is version 1.2 of the entry. See complete history

Literature

Assembly of infectious Kaposi's sarcoma-associated herpesvirus progeny requires formation of a pORF19 pentamer.

Naniima, P.Naimo, E.Koch, S.Curth, U.Alkharsah, K.R.Stroh, L.J.Binz, A.Beneke, J.M.Vollmer, B.Boning, H.Borst, E.M.Desai, P.Bohne, J.Messerle, M.Bauerfeind, R.Legrand, P.Sodeik, B.Schulz, T.F.Krey, T.

(2021) PLoS Biol 19: e3001423-e3001423

  • DOI: https://doi.org/10.1371/journal.pbio.3001423
  • Primary Citation Related Structures: 
    7NXP, 7NXQ, 7NXR

  • PubMed Abstract: 

    Herpesviruses cause severe diseases particularly in immunocompromised patients. Both genome packaging and release from the capsid require a unique portal channel occupying one of the 12 capsid vertices. Here, we report the 2.6 Å crystal structure of the pentameric pORF19 of the γ-herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) resembling the portal cap that seals this portal channel. We also present the structure of its β-herpesviral ortholog, revealing a striking structural similarity to its α- and γ-herpesviral counterparts despite apparent differences in capsid association. We demonstrate pORF19 pentamer formation in solution and provide insights into how pentamerization is triggered in infected cells. Mutagenesis in its lateral interfaces blocked pORF19 pentamerization and severely affected KSHV capsid assembly and production of infectious progeny. Our results pave the way to better understand the role of pORF19 in capsid assembly and identify a potential novel drug target for the treatment of herpesvirus-induced diseases.


  • Organizational Affiliation
    • Institute of Virology, Hannover Medical School, Hannover, Germany.

Macromolecule Content 

  • Total Structure Weight: 491.82 kDa 
  • Atom Count: 33,920 
  • Modeled Residue Count: 4,056 
  • Deposited Residue Count: 4,430 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid vertex component 2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
443Human gammaherpesvirus 8Mutation(s): 0 
UniProt
Find proteins for Q2HRB3 (Human herpesvirus 8 type P (isolate GK18))
Explore Q2HRB3 
Go to UniProtKB:  Q2HRB3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2HRB3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACT

Query on ACT



Download:Ideal Coordinates CCD File
AA [auth I]
BA [auth I]
CA [auth J]
DA [auth J]
K [auth A]
AA [auth I],
BA [auth I],
CA [auth J],
DA [auth J],
K [auth A],
L [auth A],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
Q [auth D],
R [auth D],
S [auth E],
T [auth E],
U [auth F],
V [auth F],
W [auth G],
X [auth G],
Y [auth H],
Z [auth H]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.235 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.207 (Depositor) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.51α = 90
b = 239.138β = 90
c = 264.402γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermanyGerman Center for Infection Research (DZIF) - TTU 07.704

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection