6rmm

Crystal structure of TOPBP1 BRCT4,5 in complex with a 53BP1 phosphopeptide

Method: X-RAY DIFFRACTION Dmax: 101.7 Å Quality: EXCELLENT

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

DNA topoisomerase 2-binding protein 1

Homo sapiens

UniProt Q92547

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 548–741 Chain B; UniProt 548–741 Chain C; UniProt 548–741 Chain D; UniProt 548–741 Not recorded 53BP1 × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;287.15 K;10% w/v PEG 4000, 20% v/v glycerol 0.02 M of each carboxylic acid 0.1 M MOPS/HEPES-Na pH 7.5 Resolution 3.53 Å R-free 0.234

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.

14 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOPB1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–196; UniProt 548–741 Author chain B; PDBConstruct 3–196; UniProt 548–741 Author chain C; PDBConstruct 3–196; UniProt 548–741 Author chain D; PDBConstruct 3–196; UniProt 548–741

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 6rmm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6rmm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6rmm
Deposition date deposition_date2019-05-07
Structure title titleCrystal structure of TOPBP1 BRCT4,5 in complex with a 53BP1 phosphopeptide
Keywords keywordsBRCT domain Phosphopeptide recognition, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.79
Radius of gyration Rg (electron density) rg_electron31.97
Forward intensity I(0) i0115092000.00
Molecular weight molecular_weight86509.0 kDa
Excluded volume excluded_volume109080 ų
Envelope volume envelope_volume150260 ų
Hydration-shell volume shell_volume39717 ų
Envelope diameter envelope_diameter101.8
Shell Rg shell_rg38.44
Envelope Rg envelope_rg31.44
Shape Rg shape_rg31.94
Total Rg total_rg32.65
Total atoms total_atoms6078
Residues n_residues788
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 dmax101.7
Rg (real space) rg_real32.60
Rg uncertainty (real space) rg_real_error0.82
I(0) (real space) i0_real1.1510e+08
I(0) uncertainty (real space) i0_real_error1.8180e+06
Rg (reciprocal space) rg_reciprocal32.69
I(0) (reciprocal space) i0_reciprocal115100000.0000
Solution quality estimate total_estimate0.9109
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.4
Skewness Skewness skewness0.077
Kurtosis Kurtosis kurtosis-0.634
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14750000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.971

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id6rmmA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id6rmmA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id6rmmB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id6rmmB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id6rmmC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id6rmmC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id6rmmD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id6rmmD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain

8. Citations (1)

9. Files and Curves (10)