7BGF | pdb_00007bgf

CRYSTAL STRUCTURE OF THE N-TERMINAL DIMERIC COILED COIL OF THE HUMAN CTIP PROTEIN

• PDB DOI: https://doi.org/10.2210/pdb7BGF/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-01-07 Released: 2021-06-30 
• Deposition Author(s): Morton, C.R., Pellegrini, L.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.228 (DCC) 

Starting Model: in silico

Literature

Structural basis for the coiled-coil architecture of human CtIP.

Morton, C.R., Rzechorzek, N.J., Maman, J.D., Kuramochi, M., Sekiguchi, H., Rambo, R., Sasaki, Y.C., Davies, O.R., Pellegrini, L.

(2021) Open Biol 11: 210060-210060

• PubMed: 34129781 
• DOI: https://doi.org/10.1098/rsob.210060
• Primary Citation Related Structures: 
  7BGF


• PubMed Abstract: 
  

  The DNA repair factor CtIP has a critical function in double-strand break (DSB) repair by homologous recombination, promoting the assembly of the repair apparatus at DNA ends and participating in DNA-end resection. However, the molecular mechanisms of CtIP function in DSB repair remain unclear. Here, we present an atomic model for the three-dimensional architecture of human CtIP, derived from a multi-disciplinary approach that includes X-ray crystallography, small-angle X-ray scattering (SAXS) and diffracted X-ray tracking (DXT). Our data show that CtIP adopts an extended dimer-of-dimers structure, in agreement with a role in bridging distant sites on chromosomal DNA during the recombinational repair. The zinc-binding motif in the CtIP N-terminus alters dynamically the coiled-coil structure, with functional implications for the long-range interactions of CtIP with DNA. Our results provide a structural basis for the three-dimensional arrangement of chains in the CtIP tetramer, a key aspect of CtIP function in DNA DSB repair.

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Organizational Affiliation: 
• Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Kashiwa, Japan.
Centre for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
Diamond Light Source, Didcot, Oxfordshire OX11 0DE, UK.
Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.

Biological Assembly 1  

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

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 30.55 kDa 
• Atom Count: 1,911 
• Modeled Residue Count: 220 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA endonuclease RBBP8,CtIP/RBBP8	A, B	127	Homo sapiens	Mutation(s): 2  Gene Names: RBBP8, CTIP EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99708 (Homo sapiens) Explore Q99708  Go to UniProtKB:  Q99708
PHAROS:  Q99708 GTEx:  ENSG00000101773

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.228 (DCC) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.598	α = 90
b = 86.598	β = 90
c = 42.601	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Morton, C.R., Pellegrini, L.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	104641/Z/14/Z

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description