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2d8m

Solution structure of the first BRCT domain of DNA-repair protein XRCC1

Method: SOLUTION NMR Dmax: 45.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-repair protein XRCC1

Homo sapiens

UniProt P18887

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 A； UniProt 305–420 Fragment：BRCT domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；293 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：0.89mM BRCT domain U-15N,13C; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3; 90% H2O, 10% D2O | 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.

Other PDB Difference from Current Entry 2D8M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CDZ BRCT DOMAIN FROM DNA-REPAIR PROTEIN XRCC1 Deposited 1999-03-04 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 538–633（96 aa） Fragment：C-TERMINAL BRCT DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7.0, VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.266
1XNA NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN XRCC1-N-TERMINAL DOMAIN Deposited 1999-02-27 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–183（183 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-183. RESIDUES 152-183 ARE DISORDERED AND NOT SHOWN.
Mutation：D179E No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.4；Pressure 1
NMR sample composition H2O AND D2O
Resolution not provided
1XNT NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN XRCC1-N-TERMINAL DOMAIN Deposited 1999-02-27 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–183（183 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-183. RESIDUES 152-183 ARE DISORDERED AND NOT SHOWN.
Mutation：D179E No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.4；Pressure 1
NMR sample composition H2O AND D2O
Resolution not provided
2W3O Crystal structure of the human PNKP FHA domain in complex with an XRCC1-derived phosphopeptide Deposited 2008-11-13 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 C 515–522（8 aa） Fragment：RESIDUES 515-522
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL PH 8.5, 0.25 M CACL2, 28% W/V PEG 4000, 0.2 M NDSB-221
Resolution 1.85 Å R-free 0.236
2W3O Crystal structure of the human PNKP FHA domain in complex with an XRCC1-derived phosphopeptide Deposited 2008-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 515–522（8 aa） Fragment：RESIDUES 515-522
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL PH 8.5, 0.25 M CACL2, 28% W/V PEG 4000, 0.2 M NDSB-221
Resolution 1.85 Å R-free 0.236
3K75 X-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain Deposited 2009-10-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–183（183 aa） Fragment：N-terminal domain (UNP residues 1 to 183)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20-25% PEG 3350, 0.2-0.3M Tri-potassium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.95 Å R-free 0.295
3K75 X-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain Deposited 2009-10-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–183（183 aa） Fragment：N-terminal domain (UNP residues 1 to 183)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20-25% PEG 3350, 0.2-0.3M Tri-potassium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.95 Å R-free 0.295
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–155（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–155（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–155（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–155（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–155（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–155（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 1–155（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.237
3K77 X-ray crystal structure of XRCC1 Deposited 2009-10-12 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 1–155（155 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.237
3LQC X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain Deposited 2010-02-09 Different construct 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 A 1–183（183 aa）
Not recorded NA SODIUM ION × 1 CO3 CARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20-25% PEG 3350, 0.2-0.3M TRI-POTASSIUM CITRATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.35 Å R-free 0.250
5E6Q Importin alpha binding to XRCC1 NLS peptide Deposited 2015-10-10 Different construct 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 A 241–276（36 aa） Fragment：UNP residues 241-276
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.5M Ammonium sulfate, 0.1M bis-tris propane
Resolution 2.31 Å R-free 0.208
5W7X Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide Deposited 2017-06-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 514–522（9 aa） Fragment：UNP residues 514-522
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, SITTING DROP；pH 8.5；293 K；0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000
Resolution 2.00 Å R-free 0.229
5W7X Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide Deposited 2017-06-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 514–522（9 aa） Fragment：UNP residues 514-522
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, SITTING DROP；pH 8.5；293 K；0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000
Resolution 2.00 Å R-free 0.229
5W7X Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide Deposited 2017-06-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 514–522（9 aa） Fragment：UNP residues 514-522
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, SITTING DROP；pH 8.5；293 K；0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000
Resolution 2.00 Å R-free 0.229
5W7X Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide Deposited 2017-06-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 514–522（9 aa） Fragment：UNP residues 514-522
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, SITTING DROP；pH 8.5；293 K；0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000
Resolution 2.00 Å R-free 0.229
5W7Y Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated mutated peptide Deposited 2017-06-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 514–521（8 aa） Fragment：UNP residues 514-521
Mutation：S518E 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, SITTING DROP；pH 8.5；293 K；0.6mM APLF 0.6mM XRCC1 peptide 0.1M Tris 30% PEG 1000
Resolution 2.10 Å R-free 0.237
5W7Y Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated mutated peptide Deposited 2017-06-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 514–521（8 aa） Fragment：UNP residues 514-521
Mutation：S518E 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, SITTING DROP；pH 8.5；293 K；0.6mM APLF 0.6mM XRCC1 peptide 0.1M Tris 30% PEG 1000
Resolution 2.10 Å R-free 0.237

10 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XRCC1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–123； UniProt 305–420

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 2d8m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2d8m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2d8m
Deposition date deposition_date2005-12-06
Structure title titleSolution structure of the first BRCT domain of DNA-repair protein XRCC1
Keywords keywords;parallel beta-sheet, DNA ligase III, Poly(ADP-ribose) polymerase-1, DNA polymerase beta, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.11 Å
Radius of gyration Rg (electron density) rg_electron16.27 Å
Forward intensity I(0) i01249160000.00
Molecular weight molecular_weight280240.0 kDa
Excluded volume excluded_volume344080 ų
Envelope volume envelope_volume71358 ų
Hydration-shell volume shell_volume25598 ų
Envelope diameter envelope_diameter98.8 Å
Shell Rg shell_rg30.65 Å
Envelope Rg envelope_rg24.81 Å
Shape Rg shape_rg16.26 Å
Total Rg total_rg16.67 Å
Total atoms total_atoms39120
Residues n_residues2580
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax45.8 Å
Rg (real space) rg_real16.06 Å
Rg uncertainty (real space) rg_real_error0.06 Å
I(0) (real space) i0_real1.1880e+09
I(0) uncertainty (real space) i0_real_error1.0070e+07
Rg (reciprocal space) rg_reciprocal17.22 Å
I(0) (reciprocal space) i0_reciprocal1249000000.0000
Solution quality estimate total_estimate0.6799
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.3 Å
Skewness Skewness skewness0.319
Kurtosis Kurtosis kurtosis-0.256
Angular range angular_range— – 0.4650 Å−1
Current regularization parameter α current_alpha3.0050
Highest regularization parameter α highest_alpha899000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.003; Oscil: 0.963; Stabil: 0.985; Sysdev: 0.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2d8mA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
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8. Citations (1)

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9. Files and Curves (10)