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4hyy

Filament of octameric rings of DMC1 recombinase from Homo sapiens

Method: X-RAY DIFFRACTION Dmax: 103.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Meiotic recombination protein DMC1/LIM15 homolog

Homo sapiens

UniProt Q14565

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 84–340 Chain B； UniProt 84–340 Fragment：ATPase domain No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；6% PEG 3350, 0.5 M NaCl, 0.05 M MgCl2, 0.05 M HEPES-NACl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K Resolution 2.60 Å R-free 0.246
2 Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain C； UniProt 84–340 Chain D； UniProt 84–340 Fragment：ATPase domain No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；6% PEG 3350, 0.5 M NaCl, 0.05 M MgCl2, 0.05 M HEPES-NACl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K Resolution 2.60 Å R-free 0.246
3 Protein homooligomer Homooligomer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain A； UniProt 84–340 Chain B； UniProt 84–340 Chain C； UniProt 84–340 Chain D； UniProt 84–340 Fragment：ATPase domain No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；6% PEG 3350, 0.5 M NaCl, 0.05 M MgCl2, 0.05 M HEPES-NACl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K Resolution 2.60 Å R-free 0.246

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4HYY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1V5W Crystal structure of the human Dmc1 protein Deposited 2003-11-26 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–340（340 aa）
Chain B 1–340（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；PEG2000MME, Magnesium chloride, Sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.346
1V5W Crystal structure of the human Dmc1 protein Deposited 2003-11-26 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric
Chain A 1–340（340 aa）
Chain B 1–340（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；PEG2000MME, Magnesium chloride, Sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.346
2ZJB Crystal structure of the human Dmc1-M200V polymorphic variant Deposited 2008-03-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–340（340 aa）
Chain B 1–340（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；0.1M sodium citrate, 50mM MgCl2, 8% PEG 2000 MME, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.50 Å R-free 0.351
6R3P Crystal structure of human DMC1 ATPase domain Deposited 2019-03-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 83–340（258 aa）
Chain B 83–340（258 aa）
Not recorded EDO 1,2-ETHANEDIOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；50 mM HEPES-NaOH pH 7.2, 50 mM MgCl2, 500 mM NaCl, 7.5 % PEG3350
Resolution 2.05 Å R-free 0.219
6R3P Crystal structure of human DMC1 ATPase domain Deposited 2019-03-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain C 83–340（258 aa）
Chain D 83–340（258 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 8 PG4 TETRAETHYLENE GLYCOL × 4 P6G HEXAETHYLENE GLYCOL × 8 1PE PENTAETHYLENE GLYCOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；50 mM HEPES-NaOH pH 7.2, 50 mM MgCl2, 500 mM NaCl, 7.5 % PEG3350
Resolution 2.05 Å R-free 0.219
7C98 Human DMC1 post-synaptic complexes Deposited 2020-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric
Chain A 1–340（340 aa）
Chain B 1–340（340 aa）
Chain C 1–340（340 aa）
Not recorded CA CALCIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM Tris-HCl, pH 7.5, 50 mM KCl and 1 mM dithiothreitol) containing 2 mM AMP-PNP and 5 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE；The grids were blotted for 1 sec at 22 degree C with 100% relative humidity and plunge-frozen in liquid ethane cooled by liquid nitrogen using a Vitrobot Mark IV (Thermo Fisher).
Resolution 3.47 Å
7C99 Human DMC1 post-synaptic complexes with mismatched dsDNA Deposited 2020-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric
Chain A 1–340（340 aa）
Chain B 1–340（340 aa）
Chain C 1–340（340 aa）
Not recorded CA CALCIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM Tris-HCl, pH 7.5, 50 mM KCl and 1 mM dithiothreitol) containing 2 mM AMP-PNP and 5 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE；The grids were blotted for 1 sec at 22 degree C with 100% relative humidity and plunge-frozen in liquid ethane cooled by liquid nitrogen using a Vitrobot Mark IV (Thermo Fisher).
Resolution 3.36 Å
7C9C Human DMC1 pre-synaptic complexes Deposited 2020-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: tetrameric
Chain A 1–340（340 aa）
Chain B 1–340（340 aa）
Chain C 1–340（340 aa）
Not recorded CA CALCIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM Tris-HCl, pH 7.5, 50 mM KCl and 1 mM dithiothreitol) containing 2 mM AMP-PNP and 5 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE；The grids were blotted for 1 sec at 22 degree C with 100% relative humidity and plunge-frozen in liquid ethane cooled by liquid nitrogen using a Vitrobot Mark IV (Thermo Fisher).
Resolution 3.33 Å
7CGY Human DMC1 Q244M mutant of the post-synaptic complexes Deposited 2020-07-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–340（340 aa）
Chain B 1–340（340 aa）
Chain C 1–340（340 aa）
Mutation：Q244M Mutation：Q244M Mutation：Q244M CA CALCIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM Tris-HCl, pH 7.5, 50 mM KCl and 1 mM dithiothreitol) containing 2 mM AMP-PNP and 5 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE；The grids were blotted for 1 sec at 22 degree C with 100% relative humidity and plunge-frozen in liquid ethane cooled by liquid nitrogen using a Vitrobot Mark IV (Thermo Fisher).
Resolution 3.20 Å
8QQE Crystal structure of the complex between DMC1 and the PhePP domain of BRCA2 Deposited 2023-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain A 2–340（339 aa）
Chain B 2–340（339 aa）
Not recorded MG MAGNESIUM ION × 4 CL CHLORIDE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；0.1M MES at pH 6, 2.4 M sodium formate
Resolution 3.46 Å R-free 0.261
8R2G Crystal structure of a BRCA2-DMC1 complex Deposited 2023-11-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain A 83–340（258 aa）
Chain B 83–340（258 aa）
Chain C 83–340（258 aa）
Chain D 83–340（258 aa）
Chain E 83–340（258 aa）
Chain F 83–340（258 aa）
Chain G 83–340（258 aa）
Chain H 83–340（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM HEPES-NaOH pH 7.4, 50 mM MgCl2, 500 mM NaCl, 8 % PEG 3350, 20 % glycerol
Resolution 3.45 Å R-free 0.306

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DMC1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–257； UniProt 84–340 Author chain B； PDBConstruct 1–257； UniProt 84–340 Author chain C； PDBConstruct 1–257； UniProt 84–340 Author chain D； PDBConstruct 1–257； UniProt 84–340

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4hyy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4hyy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4hyy
Deposition date deposition_date2012-11-14
Structure title titleFilament of octameric rings of DMC1 recombinase from Homo sapiens
Keywords keywordsRecA homolog, DNA strand exchange, DNA, nucleus, Recombination; RECOMBINATION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.80 Å
Radius of gyration Rg (electron density) rg_electron31.71 Å
Forward intensity I(0) i0178974000.00
Molecular weight molecular_weight107000.0 kDa
Excluded volume excluded_volume134040 ų
Envelope volume envelope_volume171880 ų
Hydration-shell volume shell_volume43905 ų
Envelope diameter envelope_diameter112.1 Å
Shell Rg shell_rg39.80 Å
Envelope Rg envelope_rg31.58 Å
Shape Rg shape_rg31.69 Å
Total Rg total_rg32.42 Å
Total atoms total_atoms7536
Residues n_residues964
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax103.3 Å
Rg (real space) rg_real32.66 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real1.7900e+08
I(0) uncertainty (real space) i0_real_error2.5830e+06
Rg (reciprocal space) rg_reciprocal32.72 Å
I(0) (reciprocal space) i0_reciprocal179000000.0000
Solution quality estimate total_estimate0.9049
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.9 Å
Skewness Skewness skewness0.196
Kurtosis Kurtosis kurtosis-0.504
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha40580000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.945
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4hyya_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)
Domain ID domain_idd4hyyb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)
Domain ID domain_idd4hyyc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)
Domain ID domain_idd4hyyd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)

CATH v4.4 (4 domains)

Domain ID domain_id4hyyA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4hyyB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4hyyC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4hyyD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)