5NWL

Crystal structure of a human RAD51-ATP filament.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.93 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.271 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.15252/embj.201798162
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

    Department of Physics and Astronomy and LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands lp212@cam.ac.uk g.j.l.wuite@vu.nl e.j.g.peterman@vu.nl.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein RAD51 homolog 1
A, B, C, D, E, F, G, H, I, J, K, L, M, N
A, B, C, D, E, F, G, H, I, J, K, L, M, N
339Homo sapiensMutation(s): 0 
Gene Names: RAD51RAD51ARECA
UniProt & NIH Common Fund Data Resources
Find proteins for Q06609 (Homo sapiens)
Explore Q06609 
Go to UniProtKB:  Q06609
PHAROS:  Q06609
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06609
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
BA [auth G],
DA [auth H],
FA [auth I],
HA [auth J],
JA [auth K],
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
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth G],
CA [auth H],
EA [auth I],
GA [auth J],
IA [auth K],
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.93 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.271 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.7α = 90
b = 128β = 90.3
c = 230.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104641/Z/14/Z

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references