Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 59.79 kDa 
• Atom Count: 3869 
• Residue Count: 449 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2BGW

XPF from Aeropyrum pernix, complex with DNA

• DOI: 10.2210/pdb2BGW/pdb
• NDB: PD0921

• Classification: HYDROLASE
• Organism(s): Aeropyrum pernix, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-01-06 Released: 2005-02-23 
• Deposition Author(s): Newman, M., Murray-Rust, J., Lally, J., Rudolf, J., Fadden, A., Knowles, P.P., White, M.F., McDonald, N.Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.263 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Literature

Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition.

Newman, M., Murray-Rust, J., Lally, J., Rudolf, J., Fadden, A., Knowles, P.P., White, M.F., McDonald, N.Q.

(2005) EMBO J 24: 895-905

• PubMed: 15719018 
• DOI: 10.1038/sj.emboj.7600581
• Primary Citation of Related Structures:  
  2BHN, 2BGW


• PubMed Abstract: 
  

The XPF/Mus81 structure-specific endonucleases cleave double-stranded DNA (dsDNA) within asymmetric branched DNA substrates and play an essential role in nucleotide excision repair, recombination and genome integrity. We report the structure of an archaeal XPF homodimer alone and bound to dsDNA. Superposition of these structures reveals a large domain movement upon binding DNA, indicating how the (HhH)(2) domain and the nuclease domain are coupled to allow the recognition of double-stranded/single-stranded DNA junctions. We identify two nonequivalent DNA-binding sites and propose a model in which XPF distorts the 3' flap substrate in order to engage both binding sites and promote strand cleavage. The model rationalises published biochemical data and implies a novel role for the ERCC1 subunit of eukaryotic XPF complexes.

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Organizational Affiliation: 

Structural Biology Laboratory, London Research Institute, Cancer Research UK, London, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XPF ENDONUCLEASE	A, B	219	Aeropyrum pernix	Mutation(s): 0  EC: 2.7.7
Find proteins for Q9YC15 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YC15  Go to UniProtKB:  Q9YC15

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*AP*TP*CP*AP*CP*AP*GP*AP*TP *GP*CP*TP*GP*A)-3'	C	15	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*GP *TP*GP*AP*TP*C)-3'	D	15	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.263 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.312	α = 90
b = 141.312	β = 90
c = 85.311	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-06 
• Released Date: 2005-02-23 
Deposition Author(s): Newman, M., Murray-Rust, J., Lally, J., Rudolf, J., Fadden, A., Knowles, P.P., White, M.F., McDonald, N.Q.

Revision History 

• Version 1.0: 2005-02-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-14
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation