Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.08 kDa 
• Atom Count: 2485 
• Residue Count: 277 
• Unique protein chains: 1

2XGU

Structure of the N-terminal domain of capsid protein from Rabbit Endogenous Lentivirus (RELIK)

• DOI: 10.2210/pdb2XGU/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Oryctolagus cuniculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-07 Released: 2010-09-22 
• Deposition Author(s): Goldstone, D.C., Taylor, I.A., Robertson, L.E., Haire, L.F., Stoye, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.218 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Literature

Structural and Functional Analysis of Prehistoric Lentiviruses Uncovers an Ancient Molecular Interface.

Goldstone, D.C., Yap, M.W., Robertson, L.E., Haire, L.F., Taylor, W.R., Katzourakis, A., Stoye, J.P., Taylor, I.A.

(2010) Cell Host Microbe 8: 248

• PubMed: 20833376 
• DOI: 10.1016/j.chom.2010.08.006
• Primary Citation of Related Structures:  
  2XGY, 2XGU, 2XGV


• PubMed Abstract: 
  

Lentiviruses are widespread in a variety of vertebrates, often associated with chronic disease states. However, until the recent discovery of the prehistoric endogenous lentiviruses in rabbits (RELIK) and lemurs (PSIV), it was thought that lentiviruses had no capacity for germline integration and were only spread horizontally in an exogenous fashion. The existence of RELIK and PSIV refuted these ideas, revealing lentiviruses to be present in a range of mammals, capable of germline integration, and far more ancient than previously thought. Using Gag sequences reconstructed from the remnants of these prehistoric lentiviruses, we have produced chimeric lentiviruses capable of infecting nondividing cells and determined structures of capsid domains from PSIV and RELIK. We show that the structures from these diverse viruses are highly similar, containing features found in modern-day lentiviruses, including a functional cyclophilin-binding loop. Together, these data provide evidence for an ancient capsid-cyclophilin interaction preserved throughout lentiviral evolution.

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Organizational Affiliation: 

Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RELIK CAPSID N-TERMINAL DOMAIN	A, B	149	Oryctolagus cuniculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.218 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87	α = 90
b = 38.68	β = 114.87
c = 84.717	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALING	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-07 
• Released Date: 2010-09-22 
Deposition Author(s): Goldstone, D.C., Taylor, I.A., Robertson, L.E., Haire, L.F., Stoye, J.P.

Revision History 

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance