1jm7

Solution structure of the BRCA1/BARD1 RING-domain heterodimer

Method: SOLUTION NMR Dmax: 70.8 Å Quality: REASONABLE

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

BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN

Homo sapiens

UniProt P38398

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–110 Fragment:RING-Domain BRCA1-ASSOCIATED RING DOMAIN PROTEIN 1 × 1 (Q99728) 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

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.

31 other PDB entries and 70 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BRCA1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–110; UniProt 1–110

BRCA1-ASSOCIATED RING DOMAIN PROTEIN 1

Homo sapiens

UniProt Q99728

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 26–140 Fragment:RING-Domain BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN × 1 (P38398) 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

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.

10 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BARD1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–115; UniProt 26–140

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 1jm7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1jm7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1jm7
Deposition date deposition_date2001-07-17
Structure title titleSolution structure of the BRCA1/BARD1 RING-domain heterodimer
Keywords keywordsBRCA1, BARD1, RING finger, zinc-binding protein, heterodimer, ubiquitin ligase, ANTITUMOR; ANTITUMOR
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier19.58
Radius of gyration Rg (electron density) rg_electron19.22
Forward intensity I(0) i01555690000.00
Molecular weight molecular_weight320560.0 kDa
Excluded volume excluded_volume395920 ų
Envelope volume envelope_volume60370 ų
Hydration-shell volume shell_volume22602 ų
Envelope diameter envelope_diameter82.8
Shell Rg shell_rg29.60
Envelope Rg envelope_rg24.06
Shape Rg shape_rg19.24
Total Rg total_rg19.33
Total atoms total_atoms44268
Residues n_residues2800
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax70.8
Rg (real space) rg_real19.69
Rg uncertainty (real space) rg_real_error0.70
I(0) (real space) i0_real1.5560e+09
I(0) uncertainty (real space) i0_real_error2.1170e+07
Rg (reciprocal space) rg_reciprocal19.67
I(0) (reciprocal space) i0_reciprocal1556000000.0000
Solution quality estimate total_estimate0.7343
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary18.9
Skewness Skewness skewness0.485
Kurtosis Kurtosis kurtosis-0.128
Angular range angular_range— – 0.4050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1989000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.616; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.702; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1jm7a_
Class classg — Small proteins
Fold Fold foldg.44 — RING/U-box
Superfamily Superfamily superfamilyg.44.1 — RING/U-box
Family Family familyg.44.1.1 — RING finger domain, C3HC4
Domain ID domain_idd1jm7b_
Class classg — Small proteins
Fold Fold foldg.44 — RING/U-box
Superfamily Superfamily superfamilyg.44.1 — RING/U-box
Family Family familyg.44.1.1 — RING finger domain, C3HC4

CATH v4.4 (2 domains)

Domain ID domain_id1jm7A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id1jm7B00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)

8. Citations (1)

9. Files and Curves (10)