SAXSdb — 7c98

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Meiotic recombination protein DMC1/LIM15 homolog

Homo sapiens

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–DNA Homooligomer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 1–340 Chain B； UniProt 1–340 Chain C； UniProt 1–340	Not recorded	;DNA (5'-D(PTPTPTPTPTPTPTPTPT)-3') ; × 1 ;DNA (5'-D(PAPAPAPAPAPAPAPAPA)-3') ; × 1 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

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 7C98	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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
4HYY Filament of octameric rings of DMC1 recombinase from Homo sapiens Deposited 2012-11-14	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 × 8 PDB declaration: octameric	Chain A 84–340（257 aa） Fragment：ATPase domain Chain B 84–340（257 aa） Fragment：ATPase domain	Not recorded	No recorded non-water small molecule	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
4HYY Filament of octameric rings of DMC1 recombinase from Homo sapiens Deposited 2012-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain C 84–340（257 aa） Fragment：ATPase domain Chain D 84–340（257 aa） Fragment：ATPase domain	Not recorded	No recorded non-water small molecule	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
4HYY Filament of octameric rings of DMC1 recombinase from Homo sapiens Deposited 2012-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric	Chain A 84–340（257 aa） Fragment：ATPase domain Chain B 84–340（257 aa） Fragment：ATPase domain Chain C 84–340（257 aa） Fragment：ATPase domain Chain D 84–340（257 aa） Fragment：ATPase domain	Not recorded	No recorded non-water small molecule	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
6R3P Crystal structure of human DMC1 ATPase domain Deposited 2019-03-20	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 × 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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
7C99 Human DMC1 post-synaptic complexes with mismatched dsDNA Deposited 2020-06-05	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 oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 13 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 1–340； UniProt 1–340 Author chain B； PDBConstruct 1–340； UniProt 1–340 Author chain C； PDBConstruct 1–340； UniProt 1–340

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7c98
Deposition date deposition_date	2020-06-05
Structure title title	Human DMC1 post-synaptic complexes
Keywords keywords	meiotic homologous recombination, DNA repair, ATPase, RECOMBINATION, RECOMBINATION-DNA complex; RECOMBINATION/DNA
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.50 Å
Radius of gyration Rg (electron density) rg_electron	32.27 Å
Forward intensity I(0) i0	203313000.00
Molecular weight molecular_weight	109520.0 kDa
Excluded volume excluded_volume	135370 Å³
Envelope volume envelope_volume	180010 Å³
Hydration-shell volume shell_volume	46501 Å³
Envelope diameter envelope_diameter	121.3 Å
Shell Rg shell_rg	39.12 Å
Envelope Rg envelope_rg	32.61 Å
Shape Rg shape_rg	32.29 Å
Total Rg total_rg	32.73 Å
Total atoms total_atoms	7656
Residues n_residues	945
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	115.4 Å
Rg (real space) rg_real	32.61 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	2.0330e+08
I(0) uncertainty (real space) i0_real_error	3.4290e+06
Rg (reciprocal space) rg_reciprocal	32.56 Å
I(0) (reciprocal space) i0_reciprocal	203300000.0000
Solution quality estimate total_estimate	0.8405
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.7 Å
Skewness Skewness skewness	0.545
Kurtosis Kurtosis kurtosis	0.146
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	51530000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.663; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Meiotic recombination protein DMC1/LIM15 homolog
Molecular weight formula_weight	37731.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7656

MKEDQVVAEEPGFQDEEESLFQDIDLLQKHGINVADIKKLKSVGICTIKGIQMTTRRALCNVKGLSEAKVDKIKEAANKLIEPGFLTAFEYSEKRKMVFHITTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRFNVDHDAVLDNVLYARAYTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAERQQKLAQMLSRLQKISEEYNVAVFVTNQMTADPGATMTFQADPKKPIGGHILAHASTTRISLRKGRGELRIAKIYDSPEMPENEATFAITAGGIGDAKE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PTPTPTPTPTPTPTPTP*T)-3') ;
Molecular weight formula_weight	2692.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TTTTTTTTT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PAPAPAPAPAPAPAPAP*A)-3') ;
Molecular weight formula_weight	2773.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

AAAAAAAAA

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	3

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.47 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	124312

fit	/app/data/saxs_computation/c9/7c98/7c98.fit
pddf	/app/data/pr_computation/c9/7c98/7c98.pr.out
profile	/app/data/saxs_computation/c9/7c98/7c98.dat

Human DMC1 post-synaptic complexes

1. Protein Identity and Related Structures Protein Identity & Related Structures

Meiotic recombination protein DMC1/LIM15 homolog

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)