4K2J

Decameric ring structure of KSHV (HHV-8) latency-associated nuclear antigen (LANA) DNA binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Molecular Basis for Oligomeric-DNA Binding and Episome Maintenance by KSHV LANA.

Domsic, J.F.Chen, H.S.Lu, F.Marmorstein, R.Lieberman, P.M.

(2013) Plos Pathog. 9: e1003672-e1003672

  • DOI: 10.1371/journal.ppat.1003672

  • PubMed Abstract: 
  • LANA is the KSHV-encoded terminal repeat binding protein essential for viral replication and episome maintenance during latency. We have determined the X-ray crystal structure of LANA C-terminal DNA binding domain (LANADBD) to reveal its capacity to ...

    LANA is the KSHV-encoded terminal repeat binding protein essential for viral replication and episome maintenance during latency. We have determined the X-ray crystal structure of LANA C-terminal DNA binding domain (LANADBD) to reveal its capacity to form a decameric ring with an exterior DNA binding surface. The dimeric core is structurally similar to EBV EBNA1 with an N-terminal arm that regulates DNA binding and is required for replication function. The oligomeric interface between LANA dimers is dispensable for single site DNA binding, but is required for cooperative DNA binding, replication function, and episome maintenance. We also identify a basic patch opposite of the DNA binding surface that is responsible for the interaction with BRD proteins and contributes to episome maintenance function. The structural features of LANADBD suggest a novel mechanism of episome maintenance through DNA-binding induced oligomeric assembly.


    Organizational Affiliation

    Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
KSHV (HHV-8) latency-associated nuclear antigen (LANA)
A, B, C, D, E, F, G, H, I, J
140Human herpesvirus 8N/A
Find proteins for Q9DUN0 (Human herpesvirus 8)
Go to UniProtKB:  Q9DUN0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, C, E, G, I, J
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.439α = 90.00
b = 175.176β = 95.30
c = 97.065γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-3000data reduction
PHENIXrefinement
CBASSdata collection
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release