6R3P | pdb_00006r3p

Crystal structure of human DMC1 ATPase domain

PDB DOI: https://doi.org/10.2210/pdb6R3P/pdb

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

Deposited: 2019-03-20 Released: 2019-04-03
Deposition Author(s): Dunce, J.M., Davies, O.R.
Funding Organization(s): Wellcome Trust, Royal Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.219 (Depositor), 0.227 (DCC)
R-Value Work:
0.194 (Depositor), 0.205 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

BRCA2 stabilises RAD51 and DMC1 nucleoprotein filaments through a conserved interaction mode.

Dunce, J.M., Davies, O.R.

(2024) Nat Commun 15: 8292-8292

PubMed: 39333100 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-52699-3
Primary Citation Related Structures:
6R3P, 8R2G

PubMed Abstract:
BRCA2 is essential for DNA repair by homologous recombination in mitosis and meiosis. It interacts with recombinases RAD51 and DMC1 to facilitate the formation of nucleoprotein filaments on resected DNA ends that catalyse recombination-mediated repair. BRCA2's BRC repeats bind and disrupt RAD51 and DMC1 filaments, whereas its PhePP motifs bind recombinases and stabilise their nucleoprotein filaments. However, the mechanism of filament stabilisation has hitherto remained unknown. Here, we report the crystal structure of a BRCA2-DMC1 complex, revealing how core interaction sites of PhePP motifs bind to recombinases. The interaction mode is conserved for RAD51 and DMC1, which selectively bind to BRCA2's two distinct PhePP motifs via subtly divergent binding pockets. PhePP motif sequences surrounding their core interaction sites protect nucleoprotein filaments from BRC-mediated disruption. Hence, we report the structural basis of how BRCA2's PhePP motifs stabilise RAD51 and DMC1 nucleoprotein filaments for their essential roles in mitotic and meiotic recombination.

Organizational Affiliation

Department of Biochemistry, University of Cambridge, Cambridge, UK.

Macromolecule Content

Total Structure Weight: 116.81 kDa
Atom Count: 8,118
Modeled Residue Count: 985
Deposited Residue Count: 1,044
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Meiotic recombination protein DMC1/LIM15 homolog	A, B, C, D	261	Homo sapiens	Mutation(s): 0 Gene Names: DMC1, DMC1H, LIM15
UniProt & NIH Common Fund Data Resources
Find proteins for Q14565 (Homo sapiens) Explore Q14565 Go to UniProtKB: Q14565
PHAROS: Q14565 GTEx: ENSG00000100206
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14565
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C]	I [auth C], J [auth D]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain I [auth C] Focus chain J [auth D]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain G [auth C] MOL2 format, chain K [auth D] MOL2 format, chain G [auth C] mmCIF format, chain K [auth D] mmCIF format, chain G [auth C]	G [auth C], K [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain K [auth D] Interactions & Density Focus chain G [auth C] Focus chain K [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.219 (Depositor), 0.227 (DCC)
R-Value Work: 0.194 (Depositor), 0.205 (DCC)
R-Value Observed: 0.195 (Depositor)

Diffraction Data:

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.49	α = 90
b = 174.49	β = 90
c = 179.57	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-04-03

Deposition Author(s):

Dunce, J.M.

Davies, O.R.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	104158/Z/14/Z
Royal Society	United Kingdom	RG170118

Revision History (Full details and data files)

Version 1.0: 2019-04-03
Type: Initial release
Version 1.1: 2019-07-10
Changes: Data collection
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-12-04
Changes: Database references, Structure summary