4HKQ | pdb_00004hkq

XMRV reverse transcriptase in complex with RNA/DNA hybrid

• PDB DOI: https://doi.org/10.2210/pdb4HKQ/pdb
• NAKB: 4HKQ

• Classification: TRANSCRIPTION/RNA/DNA
• Organism(s): Xenotropic MuLV-related virus VP62
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-10-15 Released: 2013-02-20 
• Deposition Author(s): Nowak, E., Potrzebowski, W., Konarev, P.V., Rausch, J.W., Bona, M.K., Svergun, D.I., Bujnicki, J.M., Le Grice, S.F.J., Nowotny, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.04 Å
• R-Value Free: 
  0.280 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid

Nowak, E., Potrzebowski, W., Konarev, P.V., Rausch, J.W., Bona, M.K., Svergun, D.I., Bujnicki, J.M., Le Grice, S.F., Nowotny, M.

(2013) Nucleic Acids Res 41: 3874-3887

• PubMed: 23382176 
• DOI: https://doi.org/10.1093/nar/gkt053
• Primary Citation Related Structures: 
  4HKQ


• PubMed Abstract: 
  

  A key step in proliferation of retroviruses is the conversion of their RNA genome to double-stranded DNA, a process catalysed by multifunctional reverse transcriptases (RTs). Dimeric and monomeric RTs have been described, the latter exemplified by the enzyme of Moloney murine leukaemia virus. However, structural information is lacking that describes the substrate binding mechanism for a monomeric RT. We report here the first crystal structure of a complex between an RNA/DNA hybrid substrate and polymerase-connection fragment of the single-subunit RT from xenotropic murine leukaemia virus-related virus, a close relative of Moloney murine leukaemia virus. A comparison with p66/p51 human immunodeficiency virus-1 RT shows that substrate binding around the polymerase active site is conserved but differs in the thumb and connection subdomains. Small-angle X-ray scattering was used to model full-length xenotropic murine leukaemia virus-related virus RT, demonstrating that its mobile RNase H domain becomes ordered in the presence of a substrate-a key difference between monomeric and dimeric RTs.

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Organizational Affiliation: 
• Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 90.97 kDa 
• Atom Count: 4,071 
• Modeled Residue Count: 471 
• Deposited Residue Count: 728 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H p80	A	681	Xenotropic MuLV-related virus VP62	Mutation(s): 1  EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data)
UniProt
Find proteins for A1Z651 (Xenotropic MuLV-related virus (isolate VP62)) Explore A1Z651  Go to UniProtKB:  A1Z651

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*AP*CP*AP*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*CP*AP*U)-3')	B [auth E]	25	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*GP*AP*AP*TP*CP*A*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*CP*TP*G)-3')	C [auth F]	22	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.04 Å
• R-Value Free:  0.280 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.132	α = 90
b = 98.132	β = 90
c = 201.824	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-20 
Deposition Author(s): Nowak, E., Potrzebowski, W., Konarev, P.V., Rausch, J.W., Bona, M.K., Svergun, D.I., Bujnicki, J.M., Le Grice, S.F.J., Nowotny, M.

Revision History  

• Version 1.0: 2013-02-20
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description