Biological Assembly 1  

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 260.82 kDa 
• Atom Count: 16,391 
• Modelled Residue Count: 2,124 
• Deposited Residue Count: 2,335 
• Unique protein chains: 1

 6XF9

Crystal structure of KSHV ORF68

• PDB DOI: 10.2210/pdb6XF9/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human herpesvirus 8 type M
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-06-15 Released: 2021-02-24 
• Deposition Author(s): Didychuk, A.L., Gates, S.N., Martin, A., Glaunsinger, B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.248 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 

Literature

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

• PubMed: 33554858 
• DOI: 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.

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Organizational Affiliation: 

Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Packaging protein UL32	A, B, C, D, E	467	Human herpesvirus 8 type M	Mutation(s): 0
UniProt
Find proteins for P88958 (Human herpesvirus 8 type M) Explore P88958  Go to UniProtKB:  P88958

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.248 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 
• Space Group: C 2 2 2₁
• Diffraction Data DOI: 10.15785/SBGRID/794

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.987	α = 90
b = 224.042	β = 90
c = 192.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-24 
Deposition Author(s): Didychuk, A.L., Gates, S.N., Martin, A., Glaunsinger, B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI122528
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2021-02-24
  Type: Initial release