4E89 | pdb_00004e89

Crystal Structure of RnaseH from gammaretrovirus

• PDB DOI: https://doi.org/10.2210/pdb4E89/pdb

• Classification: HYDROLASE
• Organism(s): Xenotropic MuLV-related virus VP62
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

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

• PubMed: 22724525 
• DOI: https://doi.org/10.1042/BSR20120028
• Primary Citation Related Structures: 
  4E89


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.78 kDa 
• Atom Count: 1,220 
• Modeled Residue Count: 157 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNase H	A	157	Xenotropic MuLV-related virus VP62	Mutation(s): 0  EC: 3.1.26.4
UniProt
Find proteins for A1Z651 (Xenotropic MuLV-related virus (isolate VP62)) Explore A1Z651  Go to UniProtKB:  A1Z651

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A], D [auth A], E [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.7	α = 90
b = 63.7	β = 90
c = 163.92	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations