2W18 | pdb_00002w18

Crystal structure of the C-terminal WD40 domain of human PALB2

• PDB DOI: https://doi.org/10.2210/pdb2W18/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2008-10-15 Released: 2009-07-28 
• Deposition Author(s): Oliver, A.W., Pearl, L.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.246 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Structural Basis for Recruitment of Brca2 by Palb2

Oliver, A.W., Swift, S., Lord, C.J., Ashworth, A., Pearl, L.H.

(2009) EMBO Rep 10: 990

• PubMed: 19609323 
• DOI: https://doi.org/10.1038/embor.2009.126
• Primary Citation Related Structures: 
  2W18, 3EU7


• PubMed Abstract: 
  

  The breast cancer 2, early onset protein (BRCA2) is central to the repair of DNA damage by homologous recombination. BRCA2 recruits the recombinase RAD51 to sites of damage, regulates its assembly into nucleoprotein filaments and thereby promotes homologous recombination. Localization of BRCA2 to nuclear foci requires its association with the partner and localizer of BRCA2 (PALB2), mutations in which are associated with cancer predisposition, as well as subtype N of Fanconi anaemia. We have determined the structure of the PALB2 carboxy-terminal beta-propeller domain in complex with a BRCA2 peptide. The structure shows the molecular determinants of this important protein-protein interaction and explains the effects of both cancer-associated truncating mutants in PALB2 and missense mutations in the amino-terminal region of BRCA2.

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Organizational Affiliation: 
• Cancer Research UK DNA Repair Enzymes Group, Section of Structural Biology, 237 Fulham Road, London SW3 6JB, UK. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 39.62 kDa 
• Atom Count: 2,543 
• Modeled Residue Count: 306 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PARTNER AND LOCALIZER OF BRCA2	A	356	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q86YC2 (Homo sapiens) Explore Q86YC2  Go to UniProtKB:  Q86YC2
PHAROS:  Q86YC2 GTEx:  ENSG00000083093

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.246 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.78	α = 90
b = 64.65	β = 109.65
c = 77.25	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
SHARP	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Oliver, A.W., Pearl, L.H.

Revision History  

• Version 1.0: 2009-07-28
  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: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other