Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.02 kDa 
• Atom Count: 1452 
• Residue Count: 154 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2KN7

Structure of the XPF-single strand DNA complex

• DOI: 10.2210/pdb2KN7/pdb
• NDB: 2KN7
• BMRB: 16449

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-16 Released: 2010-08-04 
• Deposition Author(s): Das, D., Folkers, G.E., van Dijk, M., Jaspers, N.G.J., Hoeijmakers, J.H.J., Kaptein, R., Boelens, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition

Das, D., Folkers, G.E., van Dijk, M., Jaspers, N.G.J., Hoeijmakers, J.H.J., Kaptein, R., Boelens, R.

(2012) Structure 20: 667-675

• PubMed: 22483113 
• DOI: 10.1016/j.str.2012.02.009
• Primary Citation of Related Structures:  
  2KN7


• PubMed Abstract: 
  

Human XPF/ERCC1 is a structure-specific DNA endonuclease that nicks the damaged DNA strand at the 5' end during nucleotide excision repair. We determined the structure of the complex of the C-terminal domain of XPF with 10 nt ssDNA. A positively charged region within the second helix of the first HhH motif contacts the ssDNA phosphate backbone. One guanine base is flipped out of register and positioned in a pocket contacting residues from both HhH motifs of XPF. Comparison to other HhH-containing proteins indicates a one-residue deletion in the second HhH motif of XPF that has altered the hairpin conformation, thereby permitting ssDNA interactions. Previous nuclear magnetic resonance studies showed that ERCC1 in the XPF-ERCC1 heterodimer can bind dsDNA. Combining the two observations gives a model that underscores the asymmetry of the human XPF/ERCC1 heterodimer in binding at an ss/ds DNA junction.

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Organizational Affiliation: 

Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair endonuclease XPF	A, D	67	Homo sapiens	Mutation(s): 0  Gene Names: XPF, ERCC4, ERCC11 EC: 3.1
Find proteins for Q92889 (Homo sapiens) Explore Q92889  Go to UniProtKB:  Q92889
NIH Common Fund Data Resources
PHAROS:  Q92889 GTEx:  ENSG00000175595

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*GP*TP*GP*GP*CP*TP*GP*A)-3')	B, C	10	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2KN7 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-16 
• Released Date: 2010-08-04 
Deposition Author(s): Das, D., Folkers, G.E., van Dijk, M., Jaspers, N.G.J., Hoeijmakers, J.H.J., Kaptein, R., Boelens, R.

Revision History 

• Version 1.0: 2010-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-07-04
  Changes: Database references