← Back to search
6hm5

Crystal structure of TOPBP1 BRCT0,1,2 in complex with a RAD9 phosphopeptide

Method: X-RAY DIFFRACTION Dmax: 82.7 Å Quality: GOOD
▼

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

DNA topoisomerase II binding protein 1

Gallus gallus

UniProt A0A1D5P3M9

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 1–289 Not recorded Cell cycle checkpoint control protein RAD9A × 1 （Q99638） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；287.15 K；100 mM bicine/Trizma base pH 8.5, 300 mM diethyleneglycol, 300 mM triethyleneglycol, 300 mM tetraethyleneglycol, 300 mM pentaethyleneglycol, 10% w/v PEG 20000 and 20% v/v PEG MME 550 Resolution 2.33 Å R-free 0.241

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A1D5P3M9_CHICK
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–290； UniProt 1–289

Cell cycle checkpoint control protein RAD9A

OrganismNot specified

UniProt Q99638

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 380–390 Non-standard monomer：Yes (specific site not provided by mmCIF) DNA topoisomerase II binding protein 1 × 1 （A0A1D5P3M9） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；287.15 K；100 mM bicine/Trizma base pH 8.5, 300 mM diethyleneglycol, 300 mM triethyleneglycol, 300 mM tetraethyleneglycol, 300 mM pentaethyleneglycol, 10% w/v PEG 20000 and 20% v/v PEG MME 550 Resolution 2.33 Å R-free 0.241

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 6HM5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3A1J Crystal structure of the human Rad9-Hus1-Rad1 complex Deposited 2009-04-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–266（266 aa） Fragment：N-terminal domain, residues 1-266
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；296 K；15% PEG 3350, 0.18M KCl, 0.16M guanidine hydrochloride, 0.33M ZWITTERGENT 3-08, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.50 Å R-free 0.282
3G65 Crystal Structure of the Human Rad9-Rad1-Hus1 DNA Damage Checkpoint Complex Deposited 2009-02-06 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–270（270 aa） Fragment：UNP residues 1-270
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Tris-HCl, 17% PEG 2000-Mme, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.272
3GGR Crystal Structure of the Human Rad9-Hus1-Rad1 complex Deposited 2009-03-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–270（270 aa） Fragment：truncated hRad9 (residues 1-270)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；8% PEG 2000 MME, 100mM Tris-HCl,200mM Trimethylamine N-oxide dihydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.20 Å R-free 0.306
6J8Y Crystal structure of the human RAD9-HUS1-RAD1-RHINO complex Deposited 2019-01-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–270（270 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350, Sodium citrate, Bis-tris propane pH 7.5
Resolution 2.40 Å R-free 0.258
7Z6H Structure of DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp Deposited 2022-03-11 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 × 8 PDB declaration: decameric
Chain A 1–391（391 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.59 Å
8GNN Crystal structure of the human RAD9-RAD1-HUS1-RAD17 complex Deposited 2022-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–270（270 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Bis-Tris propane pH 7.5, sodium citrate, PEG 3350
Resolution 2.12 Å R-free 0.263
8JZY RPA70N-RAD9 fusion Deposited 2023-07-06 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 296–314（19 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, sodium phosphate
Resolution 1.50 Å R-free 0.200
8WU8 Crystal structure of the human RAD9-RAD1(F64A/M256A/F266A)-HUS1-RHINO(88-99) complex Deposited 2023-10-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–270（270 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350, Potassium iodine
Resolution 2.81 Å R-free 0.267

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAD9A_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–11； UniProt 380–390

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 6hm5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6hm5
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6hm5
Deposition date deposition_date2018-09-12
Structure title titleCrystal structure of TOPBP1 BRCT0,1,2 in complex with a RAD9 phosphopeptide
Keywords keywordsBRCT domain phosphopeptide recognition, cell cycle; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier23.78 Å
Radius of gyration Rg (electron density) rg_electron23.54 Å
Forward intensity I(0) i015414800.00
Molecular weight molecular_weight29445.0 kDa
Excluded volume excluded_volume36802 ų
Envelope volume envelope_volume44988 ų
Hydration-shell volume shell_volume17776 ų
Envelope diameter envelope_diameter83.2 Å
Shell Rg shell_rg28.17 Å
Envelope Rg envelope_rg23.86 Å
Shape Rg shape_rg23.52 Å
Total Rg total_rg24.22 Å
Total atoms total_atoms4091
Residues n_residues258
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
▼

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

Maximum dimension Dmax dmax82.7 Å
Rg (real space) rg_real24.10 Å
Rg uncertainty (real space) rg_real_error0.83 Å
I(0) (real space) i0_real1.5410e+07
I(0) uncertainty (real space) i0_real_error2.5310e+05
Rg (reciprocal space) rg_reciprocal24.02 Å
I(0) (reciprocal space) i0_reciprocal15410000.0000
Solution quality estimate total_estimate0.7997
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.7 Å
Skewness Skewness skewness0.613
Kurtosis Kurtosis kurtosis-0.241
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4652000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.631; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.532; Smooth: 0.981
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6hm5A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id6hm5A02
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)