5NWL | pdb_00005nwl

Crystal structure of a human RAD51-ATP filament.

• PDB DOI: https://doi.org/10.2210/pdb5NWL/pdb

• Classification: RECOMBINATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-05-06 Released: 2018-03-07 
• Deposition Author(s): Pellegrini, L., Moschetti, T.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.93 Å
• R-Value Free: 
  0.317 (Depositor), 0.309 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.271 (Depositor) 

Starting Model: experimental

Literature

Two distinct conformational states define the interaction of human RAD51-ATP with single-stranded DNA.

Brouwer, I., Moschetti, T., Candelli, A., Garcin, E.B., Modesti, M., Pellegrini, L., Wuite, G.J., Peterman, E.J.

(2018) EMBO J 37

• PubMed: 29507080 
• DOI: https://doi.org/10.15252/embj.201798162
• Primary Citation Related Structures: 
  5NWL


• PubMed Abstract: 
  

  An essential mechanism for repairing DNA double-strand breaks is homologous recombination (HR). One of its core catalysts is human RAD51 (hRAD51), which assembles as a helical nucleoprotein filament on single-stranded DNA, promoting DNA-strand exchange. Here, we study the interaction of hRAD51 with single-stranded DNA using a single-molecule approach. We show that ATP-bound hRAD51 filaments can exist in two different states with different contour lengths and with a free-energy difference of ~4 k _B T per hRAD51 monomer. Upon ATP hydrolysis, the filaments convert into a disassembly-competent ADP-bound configuration. In agreement with the single-molecule analysis, we demonstrate the presence of two distinct protomer interfaces in the crystal structure of a hRAD51-ATP filament, providing a structural basis for the two conformational states of the filament. Together, our findings provide evidence that hRAD51-ATP filaments can exist in two interconvertible conformational states, which might be functionally relevant for DNA homology recognition and strand exchange.

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Organizational Affiliation: 
• Department of Physics and Astronomy and LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
Department of Biochemistry, University of Cambridge, Cambridge, UK.
Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France.
Department of Biochemistry, University of Cambridge, Cambridge, UK [e-mail] [e-mail] [e-mail].
Department of Physics and Astronomy and LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 525.57 kDa 
• Atom Count: 32,767 
• Modeled Residue Count: 4,207 
• Deposited Residue Count: 4,746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	A, B, C, D, E, F, G, H, I, J, K, L, M, N	339	Homo sapiens	Mutation(s): 0  Gene Names: RAD51, RAD51A, RECA EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q06609 (Homo sapiens) Explore Q06609  Go to UniProtKB:  Q06609
PHAROS:  Q06609 GTEx:  ENSG00000051180

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	BA [auth G], DA [auth H], FA [auth I], HA [auth J], JA [auth K], LA [auth L], NA [auth M], P [auth A], PA [auth N], R [auth B], T [auth C], V [auth D], X [auth E], Z [auth F]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	AA [auth G], CA [auth H], EA [auth I], GA [auth J], IA [auth K], KA [auth L], MA [auth M], O [auth A], OA [auth N], Q [auth B], S [auth C], U [auth D], W [auth E], Y [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.93 Å
• R-Value Free:  0.317 (Depositor), 0.309 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.271 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.7	α = 90
b = 128	β = 90.3
c = 230.1	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Pellegrini, L., Moschetti, T.

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

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description