4E89

Crystal Structure of RnaseH from gammaretrovirus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of xenotropic murine leukaemia virus-related virus (XMRV) ribonuclease H

Kim, J.H.Kang, S.Jung, S.K.Yu, K.R.Chung, S.J.Chung, B.H.Erikson, R.L.Kim, B.Y.Kim, S.J.

(2012) Biosci.Rep. 32: 455-463

  • DOI: 10.1042/BSR20120028

  • PubMed Abstract: 
  • RNase H (retroviral ribonuclease H) cleaves the phosphate backbone of the RNA template within an RNA/DNA hybrid to complete the synthesis of double-stranded viral DNA. In the present study we have determined the complete structure of the RNase H doma ...

    RNase H (retroviral ribonuclease H) cleaves the phosphate backbone of the RNA template within an RNA/DNA hybrid to complete the synthesis of double-stranded viral DNA. In the present study we have determined the complete structure of the RNase H domain from XMRV (xenotropic murine leukaemia virus-related virus) RT (reverse transcriptase). The basic protrusion motif of the XMRV RNase H domain is folded as a short helix and an adjacent highly bent loop. Structural superposition and subsequent mutagenesis experiments suggest that the basic protrusion motif plays a role in direct binding to the major groove in RNA/DNA hybrid, as well as in establishing the co-ordination among modules in RT necessary for proper function.


    Organizational Affiliation

    Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-Gu, Daejeon, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNase H
A
157Xenotropic MuLV-related virusMutation(s): 0 
Gene Names: gag-pol
Find proteins for A1Z651 (Xenotropic MuLV-related virus)
Go to UniProtKB:  A1Z651
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.239 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.700α = 90.00
b = 63.700β = 90.00
c = 163.920γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
ADSCdata collection
CNSrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-03-19 
  • Released Date: 2012-10-17 
  • Deposition Author(s): Kim, J.H., Kim, S.J.

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release