PDB-6r3p: Crystal structure of human DMC1 ATPase domain

ID or keywords:

Entry

Database: PDB / ID: 6r3p

Title

Crystal structure of human DMC1 ATPase domain

Components

Meiotic recombination protein DMC1/LIM15 homolog

Keywords

RECOMBINATION / Recombinase / Homologous recombination / Strand invasion / Meiosis

Function / homology

Function and homology information

female gamete generation / DNA recombinase assembly / chromosome organization involved in meiotic cell cycle / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / DNA strand invasion / mitotic recombination / DNA strand exchange activity / lateral element / oocyte maturation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

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

Funding support

United Kingdom, 2items

Citation

Journal: Nat Commun / Year: 2024
Title: BRCA2 stabilises RAD51 and DMC1 nucleoprotein filaments through a conserved interaction mode.
Authors: Dunce, J.M. / Davies, O.R.

History

Deposition	Mar 20, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 3, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 10, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Dec 4, 2024	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6r3p.cif.gz	571.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6r3p.ent.gz	486.5 KB	Display	PDB format
PDBx/mmJSON format	6r3p.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6r3p_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6r3p_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6r3p_validation.xml.gz	38.7 KB	Display
Data in CIF	6r3p_validation.cif.gz	53.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r3/6r3p ftp://data.pdbj.org/pub/pdb/validation_reports/r3/6r3p	HTTPS FTP

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Related structure data

Related structure data	8r2gC 4hyyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4hyy-1 4hyy-2 1v5w-1 2zjb-1 6khx-d 6l8d-d 6umx-d 5ept-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#172 - Apr 2014 RecA and Rad51 similarity (9) #121 - Jan 2010 70S Ribosomes similarity (2) #253 - Jan 2021 Expressome similarity (2) #55 - Jul 2004 DNA Ligase similarity (1) #10 - Oct 2000 Ribosome similarity (1)

Deposited unit

A: Meiotic recombination protein DMC1/LIM15 homolog

B: Meiotic recombination protein DMC1/LIM15 homolog

C: Meiotic recombination protein DMC1/LIM15 homolog

D: Meiotic recombination protein DMC1/LIM15 homolog

hetero molecules

117 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Meiotic recombination protein DMC1/LIM15 homolog

B: Meiotic recombination protein DMC1/LIM15 homolog

hetero molecules

A: Meiotic recombination protein DMC1/LIM15 homolog

B: Meiotic recombination protein DMC1/LIM15 homolog

hetero molecules

A: Meiotic recombination protein DMC1/LIM15 homolog

B: Meiotic recombination protein DMC1/LIM15 homolog

hetero molecules

A: Meiotic recombination protein DMC1/LIM15 homolog

B: Meiotic recombination protein DMC1/LIM15 homolog

hetero molecules

defined by author
Evidence: light scattering, SEC-MALS was used to confirm the octameric oligomeric state, SAXS, SEC-SAXS demonstrated that the solved crystal structure matches the structure in solution
231 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Meiotic recombination protein DMC1/LIM15 homolog

D: Meiotic recombination protein DMC1/LIM15 homolog

hetero molecules

C: Meiotic recombination protein DMC1/LIM15 homolog

D: Meiotic recombination protein DMC1/LIM15 homolog

hetero molecules

C: Meiotic recombination protein DMC1/LIM15 homolog

D: Meiotic recombination protein DMC1/LIM15 homolog

hetero molecules

C: Meiotic recombination protein DMC1/LIM15 homolog

D: Meiotic recombination protein DMC1/LIM15 homolog

hetero molecules

defined by author
Evidence: light scattering, SEC-MALS was used to confirm the octameric oligomeric state, SAXS, SEC-SAXS demonstrated that the solved crystal structure matches the structure in solution
236 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	174.490, 174.490, 179.570
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Meiotic recombination protein DMC1/LIM15 homolog Mass: 28868.811 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DMC1, DMC1H, LIM15 / Plasmid: pHAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14565

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Non-polymers , 6 types, 301 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#6: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 50 mM HEPES-NaOH pH 7.2, 50 mM MgCl2, 500 mM NaCl, 7.5 % PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9159 Å / Relative weight: 1
Reflection	Resolution: 2.05→47.49 Å / Num. obs: 86315 / % possible obs: 100 % / Redundancy: 15 % / B_iso Wilson estimate: 58.74 Å² / CC_1/2: 1 / R_pim(I) all: 0.034 / R_rim(I) all: 0.096 / Net I/σ(I): 19.5
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 15.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4545 / CC_1/2: 0.628 / R_pim(I) all: 0.72 / R_rim(I) all: 2.038 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4HYY

4hyy

Resolution: 2.05→47.011 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 23.57

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2191	8011	4.82 %	Random selection
R_work	0.1942	-	-	-
obs	0.1954	86291	99.96 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.05→47.011 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7704	0	89	293	8086

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7958
X-RAY DIFFRACTION	f_angle_d	0.478	10673
X-RAY DIFFRACTION	f_dihedral_angle_d	14.118	2981
X-RAY DIFFRACTION	f_chiral_restr	0.042	1169
X-RAY DIFFRACTION	f_plane_restr	0.003	1385

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.05-2.0733	0.3449	208	0.3133	5362	X-RAY DIFFRACTION	100
2.0733-2.0977	0.3208	264	0.2997	5258	X-RAY DIFFRACTION	100
2.0977-2.1233	0.2996	252	0.2944	5295	X-RAY DIFFRACTION	100
2.1233-2.1502	0.2953	275	0.2998	5290	X-RAY DIFFRACTION	100
2.1502-2.1785	0.3209	243	0.2702	5347	X-RAY DIFFRACTION	100
2.1785-2.2083	0.2664	239	0.2598	5193	X-RAY DIFFRACTION	100
2.2083-2.2398	0.2927	282	0.2494	5286	X-RAY DIFFRACTION	100
2.2398-2.2733	0.2919	255	0.2534	5268	X-RAY DIFFRACTION	100
2.2733-2.3088	0.2779	273	0.2474	5279	X-RAY DIFFRACTION	100
2.3088-2.3467	0.2619	302	0.2434	5229	X-RAY DIFFRACTION	100
2.3467-2.3871	0.2565	293	0.2343	5264	X-RAY DIFFRACTION	100
2.3871-2.4305	0.2452	319	0.2193	5202	X-RAY DIFFRACTION	100
2.4305-2.4773	0.2374	254	0.22	5273	X-RAY DIFFRACTION	100
2.4773-2.5278	0.2482	256	0.2235	5274	X-RAY DIFFRACTION	100
2.5278-2.5828	0.2394	268	0.2248	5272	X-RAY DIFFRACTION	100
2.5828-2.6429	0.2395	324	0.2109	5235	X-RAY DIFFRACTION	100
2.6429-2.709	0.2336	289	0.2058	5208	X-RAY DIFFRACTION	100
2.709-2.7822	0.2322	264	0.2218	5316	X-RAY DIFFRACTION	100
2.7822-2.864	0.248	246	0.2176	5291	X-RAY DIFFRACTION	100
2.864-2.9565	0.2353	249	0.2286	5268	X-RAY DIFFRACTION	100
2.9565-3.0621	0.2386	303	0.2192	5268	X-RAY DIFFRACTION	100
3.0621-3.1847	0.2296	238	0.2026	5262	X-RAY DIFFRACTION	100
3.1847-3.3296	0.2357	254	0.1966	5312	X-RAY DIFFRACTION	100
3.3296-3.5051	0.2026	264	0.1762	5244	X-RAY DIFFRACTION	100
3.5051-3.7246	0.1833	278	0.1683	5298	X-RAY DIFFRACTION	100
3.7246-4.0121	0.1764	254	0.1571	5300	X-RAY DIFFRACTION	100
4.0121-4.4155	0.1692	289	0.1382	5215	X-RAY DIFFRACTION	100
4.4155-5.0538	0.1663	198	0.1447	5358	X-RAY DIFFRACTION	100
5.0538-6.3648	0.2345	308	0.1772	5241	X-RAY DIFFRACTION	100
6.3648-47.0229	0.2092	270	0.2028	5250	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.9201	-0.5801	0.5387	5.3372	0.0897	1.1006	0.0269	-0.0762	-0.2146	0.0431	-0.0244	0.2057	0.0916	-0.0813	0.0224	0.394	-0.0371	-0.0396	0.3844	-0.0441	0.3243	34.6045	23.8802	71.4306
2	5.2242	0.3856	1.8939	6.9637	1.0824	8.813	-0.1114	0.8754	-0.2525	-1.2944	0.2853	0.3462	-0.0931	-0.7247	-0.2139	0.8603	0.0174	-0.048	0.588	-0.0075	0.3497	36.0134	24.9413	51.4052
3	6.8828	-0.4978	0.1239	2.7481	0.537	1.062	-0.1153	0.1378	0.034	0.0705	0.1088	-0.0292	0.0159	0.0129	0.025	0.3607	-0.0126	-0.0147	0.4045	-0.0522	0.2983	7.7492	41.3449	71.3158
4	5.2634	0.9253	4.2558	8.0998	3.6392	7.6158	0.3417	1.1265	-0.0853	-0.8092	0.0344	-0.2095	0.335	-0.5034	-0.3719	0.6604	-0.0546	-0.0263	1.1242	0.0688	0.4392	7.7506	43.2239	51.5042
5	4.6907	-0.3377	0.2466	2.1991	-0.5874	1.3037	0.0304	0.3547	0.1152	-0.1201	-0.0241	0.0632	0.0709	-0.0262	-0.0013	0.3278	-0.0216	0.0084	0.3036	0.0055	0.2544	83.1749	45.6301	70.866
6	2.0041	-0.8985	-3.3696	8.6364	-2.7752	8.0502	0.4657	0.6896	0.2854	-1.1168	-0.1548	0.1097	-0.2789	0.7429	-0.2933	0.6788	0.0265	-0.0246	1.1333	-0.0699	0.39	83.1371	44.2606	51.2499
7	3.0457	-0.8847	-0.087	3.7249	-0.3364	1.269	0.0851	0.1376	0.206	-0.1088	-0.0843	-0.1857	-0.0431	0.0022	0.008	0.2883	-0.0455	0.015	0.3214	0.0088	0.2583	54.8105	60.7147	71.0282
8	5.8288	0.4216	-1.3929	6.6247	1.0213	8.5368	0.0727	1.234	-0.0016	-1.0035	0.1719	-0.3529	0.2237	0.7329	-0.2184	0.7497	0.0532	0.0008	0.7151	-0.0148	0.3018	53.3635	59.4463	51.0212

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 82:300)
2	X-RAY DIFFRACTION	2	(chain A and resid 301:340)
3	X-RAY DIFFRACTION	3	(chain B and resid 83:300)
4	X-RAY DIFFRACTION	4	(chain B and resid 301:340)
5	X-RAY DIFFRACTION	5	(chain C and resid 81:301)
6	X-RAY DIFFRACTION	6	(chain C and resid 302:338)
7	X-RAY DIFFRACTION	7	(chain D and resid 82:300)
8	X-RAY DIFFRACTION	8	(chain D and resid 301:340)

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