Crystal structure of KSHV ORF68

Experimental Data Snapshot

  • Resolution: 2.22 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


A pentameric protein ring with novel architecture is required for herpesviral packaging.

Didychuk, A.L.Gates, S.N.Gardner, M.R.Strong, L.M.Martin, A.Glaunsinger, B.A.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.62261
  • Primary Citation of Related Structures:  
    6XF9, 6XFA

  • PubMed Abstract: 

    Genome packaging in large double-stranded DNA viruses requires a powerful molecular motor to force the viral genome into nascent capsids, which involves essential accessory factors that are poorly understood. Here, we present structures of two such accessory factors from the oncogenic herpesviruses Kaposi's sarcoma-associated herpesvirus (KSHV; ORF68) and Epstein-Barr virus (EBV; BFLF1). These homologous proteins form highly similar homopentameric rings with a positively charged central channel that binds double-stranded DNA. Mutation of individual positively charged residues within but not outside the channel ablates DNA binding, and in the context of KSHV infection, these mutants fail to package the viral genome or produce progeny virions. Thus, we propose a model in which ORF68 facilitates the transfer of newly replicated viral genomes to the packaging motor.

  • Organizational Affiliation

    Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Packaging protein UL32
A, B, C, D, E
467Human herpesvirus 8 type MMutation(s): 0 
Find proteins for P88958 (Human herpesvirus 8 type M)
Explore P88958 
Go to UniProtKB:  P88958
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP88958
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth B]
J [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth D],
P [auth D],
Q [auth D],
R [auth E],
S [auth E],
T [auth E]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.987α = 90
b = 224.042β = 90
c = 192.27γ = 90
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
STARANISOdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI122528
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-04-03
    Changes: Refinement description