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1d4u

INTERACTIONS OF HUMAN NUCLEOTIDE EXCISION REPAIR PROTEIN XPA WITH RPA70 AND DNA: CHEMICAL SHIFT MAPPING AND 15N NMR RELAXATION STUDIES

Method: SOLUTION NMR Dmax: 70.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NUCLEOTIDE EXCISION REPAIR PROTEIN XPA (XPA-MBD)

Homo sapiens

UniProt P23025

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 40–150 Fragment：XPA-MBD ZN ZINC ION × 1 SOLUTION NMR NMR measurement conditions：pH 7.3；303 K；Ionic strength (raw mmCIF value) 150mM；Pressure 1ATM. NMR sample composition：50MM TRIS-HCL;PH7.3,150MM KCL, 25MM DTT 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 1D4U Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1XPA SOLUTION STRUCTURE OF THE DNA-AND RPA-BINDING DOMAIN OF THE HUMAN REPAIR FACTOR XPA, NMR, 1 STRUCTURE Deposited 1998-07-06 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 98–219（122 aa） Fragment：MF122, RESIDUES 98-219
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7.3；303 K；Ionic strength (raw mmCIF value) 150mM KCL；Pressure 1
NMR sample composition 50MM D-TRIS HCL
Resolution not provided
28KE Cryo-EM structure of the human holo-TFIIH-XPC-XPA complex bound to bulky lesion-mimic DNA Deposited 2026-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain N 1–273（273 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.60 Å
2JNW Solution structure of a ERCC1-XPA heterodimer Deposited 2007-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 67–80（14 aa） Fragment：ERCC1-binding region, residues 67-80
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；295 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 0.25 mM [U-100% 13C; U-100% 15N] ERCC1, 20 mM Tris-HCl pH 7.2, 50 mM NaCl, 2 mM beta-mercaptoethanol, 0.1 mM EDTA, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.25 mM [U-100% 15N, 100% 2H] ERCC1, 20 mM Tris-HCl pH 7.2, 50 mM NaCl, 2 mM beta-mercaptoethanol, 0.1 mM EDTA, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
6J44 Crystal structure of the redefined DNA-binding domain of human XPA Deposited 2019-01-07 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 98–239（142 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；1.8 M Ammonium citrate tribasic
Resolution 2.06 Å R-free 0.239
6LAE Crystal structure of the DNA-binding domain of human XPA in complex with DNA Deposited 2019-11-12 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 Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 98–239（142 aa）
Chain B 98–239（142 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；289 K；20% PEG4000, 20% 2-propanol, 0.1 mM sodium citrate tribasic pH 5.6
Resolution 2.81 Å R-free 0.237
6RO4 Structure of the core TFIIH-XPA-DNA complex Deposited 2019-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain G 1–273（273 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；4 ul of sample was applied to glow-discharged grids which were blotted for 5s and plunge-frozen in liquid ethane.
Resolution 3.50 Å
7AD8 Core TFIIH-XPA-DNA complex with modelled p62 subunit Deposited 2020-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain G 1–273（273 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8EBT XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (Cy5) Deposited 2022-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 102–273（172 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8EBU XPC release from Core7-XPA-DNA (Cy5) Deposited 2022-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–273（273 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8EBX XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP) Deposited 2022-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–273（273 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8EBY XPC release from Core7-XPA-DNA (AP) Deposited 2022-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–273（273 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9PCP NER dual incision complex - NoG Deposited 2025-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain K 1–273（273 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9PD3 NER dual incision complex - DuIS Deposited 2025-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain K 1–273（273 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9PD4 NER dual incision complex - DuIM Deposited 2025-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain K 1–273（273 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9PD5 NER dual incision complex - NoF Deposited 2025-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–273（273 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
9QEC Cryo-EM structure of the XPF-ERCC1-XPA complex Deposited 2025-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–273（273 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9XYU NER complex - C7CAD.ATP Deposited 2025-08-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–273（273 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XPA_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–111； UniProt 40–150

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 1d4u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d4u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d4u
Deposition date deposition_date1999-10-06
Structure title titleINTERACTIONS OF HUMAN NUCLEOTIDE EXCISION REPAIR PROTEIN XPA WITH RPA70 AND DNA: CHEMICAL SHIFT MAPPING AND 15N NMR RELAXATION STUDIES
Keywords keywordsDNA REPAIR, LOOP-RICH DOMAIN, NMR RELAXATION, 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_guinier17.06 Å
Radius of gyration Rg (electron density) rg_electron15.89 Å
Forward intensity I(0) i03718120.00
Molecular weight molecular_weight13315.0 kDa
Excluded volume excluded_volume16542 ų
Envelope volume envelope_volume20409 ų
Hydration-shell volume shell_volume11665 ų
Envelope diameter envelope_diameter70.6 Å
Shell Rg shell_rg20.60 Å
Envelope Rg envelope_rg16.63 Å
Shape Rg shape_rg15.86 Å
Total Rg total_rg16.93 Å
Total atoms total_atoms1832
Residues n_residues111
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 dmax70.6 Å
Rg (real space) rg_real17.09 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real3.7180e+06
I(0) uncertainty (real space) i0_real_error4.7930e+04
Rg (reciprocal space) rg_reciprocal17.08 Å
I(0) (reciprocal space) i0_reciprocal3718000.0000
Solution quality estimate total_estimate0.7552
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.5 Å
Skewness Skewness skewness0.417
Kurtosis Kurtosis kurtosis0.224
Angular range angular_range— – 0.4650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha548200.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.413; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.578; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1d4ua1
Class classa — All alpha proteins
Fold Fold folda.6 — Putative DNA-binding domain
Superfamily Superfamily superfamilya.6.1 — Putative DNA-binding domain
Family Family familya.6.1.2 — DNA repair factor XPA DNA- and RPA-binding domain, C-terminal subdomain
Domain ID domain_idd1d4ua2
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.5 — DNA repair factor XPA DNA- and RPA-binding domain, N-terminal subdomain

CATH v4.4 (1 domains)

Domain ID domain_id1d4uA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology530 — Nucleotide Excision Repair Protein XPA (XPA-MBD); B Chain A
Homologous superfamily homologous superfamily10 — XPA C-terminal domain
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8. Citations (1)

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9. Files and Curves (10)