3VU9 | pdb_00003vu9

Crystal Structure of Psy3-Csm2 complex

PDB DOI: https://doi.org/10.2210/pdb3VU9/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-06-23 Released: 2013-04-10
Deposition Author(s): Tawaramoto, M., Sasanuma, H., Hosaka, H., Lao, J.P., Sanda, E., Suzuki, M., Yamashita, E., Hunter, N., Shinohara, M., Nakagawa, A., Shinohara, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.231 (Depositor), 0.179 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

A new protein complex promoting the assembly of Rad51 filaments

Sasanuma, H., Tawaramoto, M.S., Lao, J.P., Hosaka, H., Sanda, E., Suzuki, M., Yamashita, E., Hunter, N., Shinohara, M., Nakagawa, A., Shinohara, A.

(2013) Nat Commun 4: 1676-1676

PubMed: 23575680 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/ncomms2678
Primary Citation Related Structures:
3VU9

PubMed Abstract:
During homologous recombination, eukaryotic RecA homologue Rad51 assembles into a nucleoprotein filament on single-stranded DNA to catalyse homologous pairing and DNA-strand exchange with a homologous template. Rad51 nucleoprotein filaments are highly dynamic and regulated via the coordinated actions of various accessory proteins including Rad51 mediators. Here, we identify a new Rad51 mediator complex. The PCSS complex, comprising budding yeast Psy3, Csm2, Shu1 and Shu2 proteins, binds to recombination sites and is required for Rad51 assembly and function during meiosis. Within the hetero-tetramer, Psy3-Csm2 constitutes a core sub-complex with DNA-binding activity. In vitro, purified Psy3-Csm2 stabilizes the Rad51-single-stranded DNA complex independently of nucleotide cofactor. The mechanism of Rad51 stabilization is inferred by our high-resolution crystal structure, which reveals Psy3-Csm2 to be a structural mimic of the Rad51-dimer, a fundamental unit of the Rad51-filament. Together, these results reveal a novel molecular mechanism for this class of Rad51-mediators, which includes the human Rad51 paralogues.

Organizational Affiliation

Institute for Protein Research, Graduate School of Science, Osaka University, Suita 565-0871, Japan.

Macromolecule Content

Total Structure Weight: 53.67 kDa
Atom Count: 3,651
Modeled Residue Count: 406
Deposited Residue Count: 458
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platinum sensitivity protein 3	A	245	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: PSY3, YLR376C, L8039.17
UniProt
Find proteins for Q12318 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12318 Go to UniProtKB: Q12318
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12318
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosome segregation in meiosis protein 2	B	213	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: CSM2, YIL132C
UniProt
Find proteins for P40465 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40465 Go to UniProtKB: P40465
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40465
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B], D [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.231 (Depositor), 0.179 (DCC)
R-Value Work: 0.182 (Depositor), 0.182 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.56	α = 90
b = 50.403	β = 102.92
c = 76.35	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-04-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-10
Type: Initial release
Version 1.1: 2013-06-26
Changes: Database references
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Derived calculations