2XGY

Complex of Rabbit Endogenous Lentivirus (RELIK)Capsid with Cyclophilin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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 lentivirus ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RELIK CAPSID N-TERMINAL DOMAINA149Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE AB173Homo sapiensMutation(s): 0 
Gene Names: PPIACYPA
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
NIH Common Fund Data Resources
PHAROS  P62937
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.158α = 90
b = 117.158β = 90
c = 49.655γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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