3VIQ | pdb_00003viq

Crystal structure of Swi5-Sfr1 complex from fission yeast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.266 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3VIQ

This is version 1.1 of the entry. See complete history

Literature

Mechanistic insights into the activation of Rad51-mediated strand exchange from the structure of a recombination activator, the Swi5-Sfr1 complex

Kuwabara, N.Murayama, Y.Hashimoto, H.Kokabu, Y.Ikeguchi, M.Sato, M.Mayanagi, K.Tsutsui, Y.Iwasaki, H.Shimizu, T.

(2012) Structure 20: 440-449

  • DOI: https://doi.org/10.1016/j.str.2012.01.005
  • Primary Citation Related Structures: 
    3VIQ, 3VIR

  • PubMed Abstract: 

    Rad51 forms a helical filament on single-stranded DNA and promotes strand exchange between two homologous DNA molecules during homologous recombination. The Swi5-Sfr1 complex interacts directly with Rad51 and stimulates strand exchange. Here we describe structural and functional aspects of the complex. Swi5 and the C-terminal core domain of Sfr1 form an essential activator complex with a parallel coiled-coil heterodimer joined firmly together via two previously uncharacterized leucine-zipper motifs and a bundle. The resultant coiled coil is sharply kinked, generating an elongated crescent-shaped structure suitable for transient binding within the helical groove of the Rad51 filament. The N-terminal region of Sfr1, meanwhile, has an interface for binding of Rad51. Our data suggest that the snug fit resulting from the complementary geometry of the heterodimer activates the Rad51 filament and that the N-terminal domain of Sfr1 plays a role in the efficient recruitment of the Swi5-Sfr1 complex to the Rad51 filaments.


  • Organizational Affiliation
    • Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecule Content 

  • Total Structure Weight: 48.61 kDa 
  • Atom Count: 3,431 
  • Modeled Residue Count: 393 
  • Deposited Residue Count: 414 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Swi5-dependent recombination DNA repair protein 1
A, C
122Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: sfr1
UniProt
Find proteins for Q9USV1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9USV1 
Go to UniProtKB:  Q9USV1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9USV1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Mating-type switching protein swi5
B, D
85Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: swi5
UniProt
Find proteins for Q9UUB7 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9UUB7 
Go to UniProtKB:  Q9UUB7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UUB7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
I [auth C]
J [auth C]
K [auth C]
E [auth A],
F [auth A],
I [auth C],
J [auth C],
K [auth C],
L [auth C],
M [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3

Query on NO3



Download:Ideal Coordinates CCD File
G [auth A]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.266 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.159α = 90
b = 128.682β = 90
c = 59.97γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHELXSphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations