SAXSdb — 6lae

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

DNA repair protein complementing XP-A cells

Homo sapiens

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 98–239 Chain B； UniProt 98–239	Not recorded	;DNA (5'-D(PGPCPAPTPCPTPCPGPCPCPT)-3') ; × 1 ;DNA (5'-D(PTPGPGPCPGPAPGPAPTPGPC)-3') ; × 1 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

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 6LAE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D4U INTERACTIONS OF HUMAN NUCLEOTIDE EXCISION REPAIR PROTEIN XPA WITH RPA70 AND DNA: CHEMICAL SHIFT MAPPING AND 15N NMR RELAXATION STUDIES Deposited 1999-10-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–150（111 aa） Fragment：XPA-MBD	Not recorded	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
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 mutation/modification 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 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 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 mutation/modification Different oligomeric state Different ligand/ion 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
6RO4 Structure of the core TFIIH-XPA-DNA complex Deposited 2019-05-10	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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 4–145； UniProt 98–239 Author chain B； PDBConstruct 4–145； UniProt 98–239

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6lae
Deposition date deposition_date	2019-11-12
Structure title title	Crystal structure of the DNA-binding domain of human XPA in complex with DNA
Keywords keywords	Protein-DNA complex, nucleotide excision repair, DNA repair, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	23.39 Å
Radius of gyration Rg (electron density) rg_electron	22.72 Å
Forward intensity I(0) i0	27584800.00
Molecular weight molecular_weight	34684.0 kDa
Excluded volume excluded_volume	41116 Å³
Envelope volume envelope_volume	56626 Å³
Hydration-shell volume shell_volume	21451 Å³
Envelope diameter envelope_diameter	74.6 Å
Shell Rg shell_rg	28.67 Å
Envelope Rg envelope_rg	22.68 Å
Shape Rg shape_rg	22.65 Å
Total Rg total_rg	23.60 Å
Total atoms total_atoms	2392
Residues n_residues	254
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	71.8 Å
Rg (real space) rg_real	23.33 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	2.7580e+07
I(0) uncertainty (real space) i0_real_error	3.3750e+05
Rg (reciprocal space) rg_reciprocal	23.34 Å
I(0) (reciprocal space) i0_reciprocal	27590000.0000
Solution quality estimate total_estimate	0.9141
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.196
Kurtosis Kurtosis kurtosis	-0.590
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1795000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA repair protein complementing XP-A cells
Molecular weight formula_weight	17473.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2398

GSHMEFDYVICEECGKEFMDSYLMNHFDLPTCDNCRDADDKHKLITKTEAKQEYLLKDCDLEKREPPLKFIVKKNPHHSQWGDMKLYLKLQIVKRSLEVWGSQEALEEAKEVRQENREKMKQKKFDKKVKELRRAVRSSVWKRET

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PGPCPAPTPCPTPCPGPCPCP*T)-3') ;
Molecular weight formula_weight	3285.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GCATCTCGCCT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PTPGPGPCPGPAPGPAPTPGP*C)-3') ;
Molecular weight formula_weight	3414.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TGGCGAGATGC

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6laeA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	530 — Nucleotide Excision Repair Protein XPA (XPA-MBD); B Chain A
Homologous superfamily homologous superfamily	10 — XPA C-terminal domain

Domain ID domain_id	6laeB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	530 — Nucleotide Excision Repair Protein XPA (XPA-MBD); B Chain A
Homologous superfamily homologous superfamily	10 — XPA C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	69.112 Å
Unit-cell length b length_b	69.112 Å
Unit-cell length c length_c	63.938 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.810 Å
Low-resolution limit resolution_low	43.700 Å
R factor r_factor	0.2198
R_work r_work	0.2185
R_free r_free	0.2369

fit	/app/data/saxs_computation/la/6lae/6lae.fit
pddf	/app/data/pr_computation/la/6lae/6lae.pr.out
profile	/app/data/saxs_computation/la/6lae/6lae.dat

Crystal structure of the DNA-binding domain of human XPA in complex with DNA

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

DNA repair protein complementing XP-A cells

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)