SAXSdb — 6m14

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

BRCA1-associated RING domain protein 1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 568–777	Mutation：V695L	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES pH 6.5, 0.2 M ammonium sulfate,22% PEG 5000	Resolution 1.88 Å R-free 0.198
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 568–777	Mutation：V695L	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES pH 6.5, 0.2 M ammonium sulfate,22% PEG 5000	Resolution 1.88 Å R-free 0.198

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 6M14	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JM7 Solution structure of the BRCA1/BARD1 RING-domain heterodimer Deposited 2001-07-17	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 × 2 PDB declaration: dimeric	Chain B 26–140（115 aa） Fragment：RING-Domain	Not recorded	ZN ZINC ION × 4	SOLUTION NMR NMR measurement conditions pH 6.8；315 K；Ionic strength (raw mmCIF value) 0.2M NaCl；Pressure ambient NMR measurement conditions pH 6.8；315 K；Ionic strength (raw mmCIF value) 0.2M NaCl；Pressure ambient NMR measurement conditions pH 6.8；315 K；Ionic strength (raw mmCIF value) 0.2M NaCl；Pressure ambient NMR measurement conditions pH 6.8；315 K；Ionic strength (raw mmCIF value) 0.2M NaCl；Pressure ambient NMR sample composition sample 1: 0.8-1.1mM U-15N,13C BRCA1; unlabeled BARD1, 25mM sodium phosphate, 0.2M NaCl, 2mM DTT. Sample 2: 0.8-1.1mM U-15N,13C BARD1; unlabeled BRCA1, 25mM sodium phosphate, 0.2M NaCl, 2mM DTT. Sample 3: 0.8-1.1mM U-15N,13C,85%-2H BRCA1; unlabeled BARD1, 25mM sodium phosphate, 0.2M NaCl, 2mM DTT. SAMPLE 4: 0.8-1.1mM U-15N,13C,85%-2H BARD1; unlabeled BRCA,1 25mM sodium phosphate, 0.2M NaCl, 2mM DTT. \| 90% H2O/10% D2O NMR sample composition 0.8-1.1mM U-15N,13C BARD1; unlabeled BRCA1 25mM sodium phosphate 0.2M NaCl 2mM DTT \| 90% H2O/10% D2O NMR sample composition 0.8-1.1mM U-15N,13C,85%-2H BRCA1; unlabeled BARD1 25mM sodium phosphate 0.2M NaCl 2mM DTT \| 90% H2O/10% D2O NMR sample composition 0.8-1.1mM U-15N,13C,85%-2H BARD1; unlabeled BRCA1 25mM sodium phosphate 0.2M NaCl 2mM DTT \| 90% H2O/10% D2O	Resolution not provided
2NTE Crystal Structure of the BARD1 BRCT Domains Deposited 2006-11-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 568–777（210 aa） Fragment：BRCT domain	Not recorded	SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100mM MES, 20% PEG 8K, 150mM Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.247
2NTE Crystal Structure of the BARD1 BRCT Domains Deposited 2006-11-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 568–777（210 aa） Fragment：BRCT domain	Not recorded	SO4 SULFATE ION × 1 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100mM MES, 20% PEG 8K, 150mM Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.247
2R1Z Crystal Structure of the BARD1 BRCT Repeat Deposited 2007-08-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 569–777（209 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；pSDDE peptide, 20% PEG 3350, 0.2 M ammonium chloride, 100 mM NaCl, 5 mM tris-HCl, 1 mM DTT, pH 7.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.10 Å R-free 0.262
2R1Z Crystal Structure of the BARD1 BRCT Repeat Deposited 2007-08-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 569–777（209 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；pSDDE peptide, 20% PEG 3350, 0.2 M ammonium chloride, 100 mM NaCl, 5 mM tris-HCl, 1 mM DTT, pH 7.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.10 Å R-free 0.262
3C5R Crystal Structure of the BARD1 Ankyrin Repeat Domain and Its Functional Consequences Deposited 2008-02-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 425–555（131 aa） Fragment：BARD1 Ankyrin Repeat Domain (UNP residues 425-555)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 Mg Chloride, 0.1 M Tris Hydrochloride pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.268
3C5R Crystal Structure of the BARD1 Ankyrin Repeat Domain and Its Functional Consequences Deposited 2008-02-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 425–555（131 aa） Fragment：BARD1 Ankyrin Repeat Domain (UNP residues 425-555)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 Mg Chloride, 0.1 M Tris Hydrochloride pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.268
3C5R Crystal Structure of the BARD1 Ankyrin Repeat Domain and Its Functional Consequences Deposited 2008-02-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 425–555（131 aa） Fragment：BARD1 Ankyrin Repeat Domain (UNP residues 425-555) Chain B 425–555（131 aa） Fragment：BARD1 Ankyrin Repeat Domain (UNP residues 425-555)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 Mg Chloride, 0.1 M Tris Hydrochloride pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.268
3FA2 Crystal Structure of the BRCA1 Associated Ring Domain (BARD1) Tandem BRCT Domains Deposited 2008-11-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 566–777（212 aa） Fragment：Tandem BRCT Domains	Not recorded	PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M MES 15% w/v PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.298
3FA2 Crystal Structure of the BRCA1 Associated Ring Domain (BARD1) Tandem BRCT Domains Deposited 2008-11-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 566–777（212 aa） Fragment：Tandem BRCT Domains	Not recorded	PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M MES 15% w/v PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.298
7E8I Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Deposited 2021-03-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 425–777（353 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7JZV Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Deposited 2020-09-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric	Chain B 26–140（115 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7LYB Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Deposited 2021-03-06	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 Heteromer；Protein × 11 PDB declaration: tridecameric	Chain N 26–122（97 aa） Fragment：RING domain (UNP residues 26-122)	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å
7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain N 415–777（363 aa） Fragment：Ankyrine repeat domain and the tandem BRCT domain (UNP residues 415-777)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
8GRQ Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome Deposited 2022-09-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain M 26–117（92 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.87 Å

10 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BARD1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–210； UniProt 568–777 Author chain B； PDBConstruct 1–210； UniProt 568–777

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	6m14
Deposition date deposition_date	2020-02-24
Structure title title	Crystal Structure of the BARD1 BRCT Mutant
Keywords keywords	BRCT, disease mutation, OLA1, ANTITUMOR PROTEIN, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	25.89 Å
Radius of gyration Rg (electron density) rg_electron	25.11 Å
Forward intensity I(0) i0	37129900.00
Molecular weight molecular_weight	48158.0 kDa
Excluded volume excluded_volume	60767 Å³
Envelope volume envelope_volume	75461 Å³
Hydration-shell volume shell_volume	25724 Å³
Envelope diameter envelope_diameter	94.8 Å
Shell Rg shell_rg	31.38 Å
Envelope Rg envelope_rg	25.17 Å
Shape Rg shape_rg	25.07 Å
Total Rg total_rg	25.95 Å
Total atoms total_atoms	6791
Residues n_residues	418
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	92.0 Å
Rg (real space) rg_real	25.92 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	3.7130e+07
I(0) uncertainty (real space) i0_real_error	6.3010e+05
Rg (reciprocal space) rg_reciprocal	25.91 Å
I(0) (reciprocal space) i0_reciprocal	37130000.0000
Solution quality estimate total_estimate	0.8593
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.2 Å
Skewness Skewness skewness	0.376
Kurtosis Kurtosis kurtosis	-0.178
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14920000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.756; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	BRCA1-associated RING domain protein 1
Molecular weight formula_weight	24116.9 kDa
EC 编号 ec_number	2.3.2.27
Mutation mutation	V695L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	7140

GPLVLIGSGLSSEQQKMLSELAVILKAKKYTEFDSTVTHVVVPGDAVQSTLKCMLGILNGCWILKFEWVKACLRRKVCEQEEKYEIPEGPRRSRLNREQLLPKLFDGCYFYLWGTFKHHPKDNLIKLLTAGGGQILSRKPKPDSDVTQTINTVAYHARPDSDQRFCTQYIIYEDLCNYHPERVRQGKVWKAPSSWFIDCVMSFELLPLDS

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 BL21

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	349

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8. Citations (1)

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Unit-cell length a length_a	57.850 Å
Unit-cell length b length_b	75.254 Å
Unit-cell length c length_c	116.824 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	27.754 Å
R factor r_factor	0.1710
R_work r_work	0.1699
R_free r_free	0.1975

fit	/app/data/saxs_computation/m1/6m14/6m14.fit
pddf	/app/data/pr_computation/m1/6m14/6m14.pr.out
profile	/app/data/saxs_computation/m1/6m14/6m14.dat

Crystal Structure of the BARD1 BRCT Mutant

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

BRCA1-associated RING domain protein 1

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

Refinement Refinement

Diffraction experiment Diffraction