Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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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: 59792.55 
• Atom Count: 3862 
• Residue Count: 468 
• 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): synthetic construct, Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
• Expression System: Escherichia coli BL21(DE3)


• 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: 2.8 Å
• R-Value Free: 0.263 
• R-Value Work: 0.223 

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


• 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

Find similar proteins by: Sequence  |  Structure

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

Entity ID: 2
Molecule	Chains	Length	Organism
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
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 & Interactions
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: 2.8 Å
• R-Value Free: 0.263 
• R-Value Work: 0.223 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 141.312	α = 90.00
b = 141.312	β = 90.00
c = 85.311	γ = 120.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-03-14
  Type: Database references, Source and taxonomy, Structure summary
• Version 1.4: 2019-05-08
  Type: Data collection, Experimental preparation