3NR6 | pdb_00003nr6

Crystal structure of xenotropic murine leukemia virus-related virus (XMRV) protease

• PDB DOI: https://doi.org/10.2210/pdb3NR6/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Xenotropic MuLV-related virus VP62
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-30 Released: 2011-02-02 
• Deposition Author(s): Lubkowski, J., Li, M., Gustchina, A., Zhou, D., Dauter, Z., Wlodawer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.233 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of XMRV protease differs from the structures of other retropepsins.

Li, M., Dimaio, F., Zhou, D., Gustchina, A., Lubkowski, J., Dauter, Z., Baker, D., Wlodawer, A.

(2011) Nat Struct Mol Biol 18: 227-229

• PubMed: 21258323 
• DOI: https://doi.org/10.1038/nsmb.1964
• Primary Citation Related Structures: 
  3NR6


• PubMed Abstract: 
  

  Using energy and density guided Rosetta refinement to improve molecular replacement, we determined the crystal structure of the protease encoded by xenotropic murine leukemia virus-related virus (XMRV). Despite overall similarity of XMRV protease to other retropepsins, the topology of its dimer interface more closely resembles those of the monomeric, pepsin-like enzymes. Thus, XMRV protease may represent a distinct branch of the aspartic protease family.

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Organizational Affiliation: 
• Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, Maryland, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.82 kDa 
• Atom Count: 1,883 
• Modeled Residue Count: 234 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease p14	A, B	132	Xenotropic MuLV-related virus VP62	Mutation(s): 0  Gene Names: gag-pol EC: 3.4.23
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
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.233 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.915	α = 90
b = 63.915	β = 90
c = 106.509	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
Rosetta	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
Rosetta	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-02 
Deposition Author(s): Lubkowski, J., Li, M., Gustchina, A., Zhou, D., Dauter, Z., Wlodawer, A.

Revision History  

• Version 1.0: 2011-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description