SAXSdb — 9qed

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

Protein SLX4IP

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–408	Not recorded	DNA repair endonuclease XPF × 1 （Q92889） DNA excision repair protein ERCC-1 × 1 （P07992） Structure-specific endonuclease subunit SLX4 × 1 （Q8IY92）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.20 Å

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 9QED	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9QEE Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex Deposited 2025-03-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 1–408（408 aa）	Not recorded	MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SLX4I_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–408； UniProt 1–408

DNA repair endonuclease XPF

Homo sapiens

UniProt Q92889

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–916	Not recorded	Protein SLX4IP × 1 （Q5VYV7） DNA excision repair protein ERCC-1 × 1 （P07992） Structure-specific endonuclease subunit SLX4 × 1 （Q8IY92）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.20 Å

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 9QED	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Z00 Solution structure of the C-terminal domain of ERCC1 complexed with the C-terminal domain of XPF Deposited 2005-03-01	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 823–905（83 aa） Fragment：C-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；295.5 K；Ionic strength (raw mmCIF value) 50mM phosphate, 100mM NaCl；Pressure 1 NMR sample composition 1.5mM ERCC1-XPF U-15N,13C; 50mM phosphate buffer NA: 92% H2O, 8% D2O \| 92% H2O, 8% D2O NMR sample composition 1mM ERCC1-XPF U-15N; 50mM phosphate buffer NA: 92% H2O, 8% D2O \| 92% H2O, 8% D2O	Resolution not provided
2A1J Crystal Structure of the Complex between the C-Terminal Domains of Human XPF and ERCC1 Deposited 2005-06-20	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 837–898（62 aa） Fragment：C-terminal domain	Not recorded	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；Sodium Citrate, Ammonium Sulfate, Sodium Chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.275
2A1J Crystal Structure of the Complex between the C-Terminal Domains of Human XPF and ERCC1 Deposited 2005-06-20	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 837–898（62 aa） Fragment：C-terminal domain	Not recorded	HG MERCURY (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；Sodium Citrate, Ammonium Sulfate, Sodium Chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.275
2AQ0 Solution structure of the human homodimeric dna repair protein XPF Deposited 2005-08-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 823–905（83 aa） Fragment：residues 823-905 Chain B 823–905（83 aa） Fragment：residues 823-905	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；293.6 K；Ionic strength (raw mmCIF value) 400mM NaCl；Pressure 1 NMR sample composition 1.2MM XPF U-15N,13C; 10mM phosphate; 400mM sodium chloride; 92 % h2o, 8% d2o \| 92% H2O, 8% D2O	Resolution not provided
2KN7 Structure of the XPF-single strand DNA complex Deposited 2009-08-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 842–908（67 aa） Fragment：residues in UNP 842-908 Chain D 842–908（67 aa） Fragment：residues in UNP 842-908	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；293.8 K；Ionic strength (raw mmCIF value) 80-100；Pressure ambient NMR sample composition 80mM sodium phosphate-1, 2mM sodium chloride-2, 0.005-0.010mM AEBSF protease inhibitor-3, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MUT Solution structure of the F231L mutant ERCC1-XPF dimerization region Deposited 2014-09-17	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 834–916（83 aa） Fragment：UNP residues 834-916	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；290 K；Ionic strength (raw mmCIF value) 250；Pressure ambient NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] protein_1, 0.4 mM [U-100% 13C; U-100% 15N] protein_2, 8 % D2O, 50 mM sodium phosphate, 100 mM sodium chloride, 92% H2O/8% D2O \| 92% H2O/8% D2O	Resolution not provided
6SXA XPF-ERCC1 Cryo-EM Structure, Apo-form Deposited 2019-09-25	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–916（916 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8；20 mM HEPES pH 7.8, 150 mM NaCl, 1 mM TCEP, 0.01% CHAPS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6SXB XPF-ERCC1 Cryo-EM Structure, DNA-Bound form Deposited 2019-09-25	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain F 1–916（916 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8；20 mM HEPES pH 7.8, 150 mM NaCl, 1 mM TCEP, 0.01% CHAPS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.90 Å
9PCP NER dual incision complex - NoG Deposited 2025-06-28	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric	Chain Q 1–916（916 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric	Chain Q 1–916（916 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain Q 1–916（916 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
9QEC Cryo-EM structure of the XPF-ERCC1-XPA complex Deposited 2025-03-08	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–916（916 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
9QEE Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex Deposited 2025-03-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–916（916 aa）	Not recorded	MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

12 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	XPF_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 20–935； UniProt 1–916

DNA excision repair protein ERCC-1

Homo sapiens

UniProt P07992

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–297	Not recorded	Protein SLX4IP × 1 （Q5VYV7） DNA repair endonuclease XPF × 1 （Q92889） Structure-specific endonuclease subunit SLX4 × 1 （Q8IY92）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.20 Å

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 9QED	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Z00 Solution structure of the C-terminal domain of ERCC1 complexed with the C-terminal domain of XPF Deposited 2005-03-01	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 A 220–297（78 aa） Fragment：C-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；295.5 K；Ionic strength (raw mmCIF value) 50mM phosphate, 100mM NaCl；Pressure 1 NMR sample composition 1.5mM ERCC1-XPF U-15N,13C; 50mM phosphate buffer NA: 92% H2O, 8% D2O \| 92% H2O, 8% D2O NMR sample composition 1mM ERCC1-XPF U-15N; 50mM phosphate buffer NA: 92% H2O, 8% D2O \| 92% H2O, 8% D2O	Resolution not provided
2A1I Crystal Structure of the Central Domain of Human ERCC1 Deposited 2005-06-20	Different construct 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 96–227（132 aa） Fragment：CENTRAL DOMAIN	Not recorded	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；MES, PEG 5000 MME, GLYCEROL, pH 6.5, VAPOR DIFFUSION, SITTING DROP,temperature 295K	Resolution 1.90 Å R-free 0.248
2A1J Crystal Structure of the Complex between the C-Terminal Domains of Human XPF and ERCC1 Deposited 2005-06-20	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 B 220–296（77 aa） Fragment：C-terminal domain	Not recorded	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；Sodium Citrate, Ammonium Sulfate, Sodium Chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.275
2A1J Crystal Structure of the Complex between the C-Terminal Domains of Human XPF and ERCC1 Deposited 2005-06-20	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 220–296（77 aa） Fragment：C-terminal domain	Not recorded	HG MERCURY (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；Sodium Citrate, Ammonium Sulfate, Sodium Chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.275
2JNW Solution structure of a ERCC1-XPA heterodimer Deposited 2007-02-07	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 A 96–214（119 aa） Fragment：Central domain, residues 96-214	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
2JPD Solution structure of the ERCC1 central domain Deposited 2007-05-06	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 96–219（124 aa） Fragment：residues 96-219	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；290 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition 50 mM sodium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MUT Solution structure of the F231L mutant ERCC1-XPF dimerization region Deposited 2014-09-17	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 A 220–297（78 aa） Fragment：UNP residues 220-297	Mutation：F231L	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；290 K；Ionic strength (raw mmCIF value) 250；Pressure ambient NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] protein_1, 0.4 mM [U-100% 13C; U-100% 15N] protein_2, 8 % D2O, 50 mM sodium phosphate, 100 mM sodium chloride, 92% H2O/8% D2O \| 92% H2O/8% D2O	Resolution not provided
6SXA XPF-ERCC1 Cryo-EM Structure, Apo-form Deposited 2019-09-25	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8；20 mM HEPES pH 7.8, 150 mM NaCl, 1 mM TCEP, 0.01% CHAPS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6SXB XPF-ERCC1 Cryo-EM Structure, DNA-Bound form Deposited 2019-09-25	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain G 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8；20 mM HEPES pH 7.8, 150 mM NaCl, 1 mM TCEP, 0.01% CHAPS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.90 Å
9PCP NER dual incision complex - NoG Deposited 2025-06-28	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric	Chain R 1–297（297 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 conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric	Chain R 1–295（295 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 conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain R 1–295（295 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
9QEC Cryo-EM structure of the XPF-ERCC1-XPA complex Deposited 2025-03-08	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–297（297 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
9QEE Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex Deposited 2025-03-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–297（297 aa）	Not recorded	MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

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

View Construct and Data Evidence

UniProt name	ERCC1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–297； UniProt 1–297

Structure-specific endonuclease subunit SLX4

Homo sapiens

UniProt Q8IY92

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 330–555	Not recorded	Protein SLX4IP × 1 （Q5VYV7） DNA repair endonuclease XPF × 1 （Q92889） DNA excision repair protein ERCC-1 × 1 （P07992）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.20 Å

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 9QED	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4M7C Crystal structure of the TRF2-binding motif of SLX4 in complex with the TRFH domain of TRF2 Deposited 2013-08-12	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1014–1025（12 aa） Fragment：TRF2-binding motif, UNP residues 1014-1025 Chain D 1014–1025（12 aa） Fragment：TRF2-binding motif, UNP residues 1014-1025	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；10% PEG 4000, 0.1M HEPES, pH 7.4, 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.05 Å R-free 0.262
4UYI Crystal structure of the BTB domain of human SLX4 (BTBD12) Deposited 2014-09-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 668–796（129 aa） Fragment：BTB DOMAIN (BTBD12), UNP RESIDUES 668-796	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2M MAGNESIUM CHLORIDE, 25% PEG3350, 0.1M BIS-TRIS PH 6.5	Resolution 1.86 Å R-free 0.194
4ZOU Crystal structure of the BTB domain of SLX4 Deposited 2015-05-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 669–787（119 aa） Fragment：BTB domain (UNP RESIDUES 669-787)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；277 K；4-6% PEG 6000, 0.1 M HEPES, pH 7.6, 5% glycerol	Resolution 2.15 Å R-free 0.244
7BU5 Crystal Structure of Human SLX4 and MUS81 Deposited 2020-04-04	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 B 1550–1610（61 aa） Fragment：SAP domain	Not recorded	GLY GLYCINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；277 K；25% w/v PEG 3350, 0.1M SPG (succinic acid: sodium dihydrogen phosphate: glycine, 2: 7: 7)	Resolution 1.80 Å R-free 0.206
7TUJ NMR solution structure of the phosphorylated MUS81-binding region from human SLX4 Deposited 2022-02-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1528–1613（86 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；283 K；Ionic strength (raw mmCIF value) 0.125；Pressure 1 NMR sample composition 500 uM [U-100% 13C; U-100% 15N] Phosphorylated MUS81-binding region of human SLX4, 25 mM sodium phosphate, 100 mM sodium chloride, 100 uM EDTA, 100 uM sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
9QEE Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex Deposited 2025-03-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain D 330–555（226 aa）	Not recorded	MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SLX4_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 46–271； UniProt 330–555

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	9qed
Deposition date deposition_date	2025-03-09
Structure title title	Cryo-EM structure of the XPF-ERCC1-SLX4(330-555)-SLX4IP complex
Keywords keywords	DNA repair, endonuclease, multiprotein complex, HYDROLASE; HYDROLASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	34.07 Å
Radius of gyration Rg (electron density) rg_electron	33.38 Å
Forward intensity I(0) i0	226706000.00
Molecular weight molecular_weight	124180.0 kDa
Excluded volume excluded_volume	157220 Å³
Envelope volume envelope_volume	207980 Å³
Hydration-shell volume shell_volume	51472 Å³
Envelope diameter envelope_diameter	117.5 Å
Shell Rg shell_rg	40.63 Å
Envelope Rg envelope_rg	32.76 Å
Shape Rg shape_rg	33.39 Å
Total Rg total_rg	33.94 Å
Total atoms total_atoms	8748
Residues n_residues	1088
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	110.4 Å
Rg (real space) rg_real	33.97 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	2.2670e+08
I(0) uncertainty (real space) i0_real_error	3.6390e+06
Rg (reciprocal space) rg_reciprocal	34.03 Å
I(0) (reciprocal space) i0_reciprocal	226700000.0000
Solution quality estimate total_estimate	0.8809
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.6 Å
Skewness Skewness skewness	0.281
Kurtosis Kurtosis kurtosis	-0.230
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	94530000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.887

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Protein SLX4IP
Molecular weight formula_weight	45627.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	8748

MASKKFAVKCGNFAVLVDLHILPQGSNKDTSWFSEQKKEEVCLLLKETIDSRVQEYLEVRKQHRPSNAEFTRSNPLSLKGYGFQITAYFLKRGIRLRCIRSTQNAELCVFPDRFVVCVSQLAFSRDLLASQNEDLTERVLHGVSDYFAECAESSLPPSAKLRRNALKEIVKRTETKSSVTSKSQTRRDTVETSSDSVIAEIARRRNDGQASSSPPSESMGQAKDSIKAAESHWGLPVQKLEKVNQTQPEDTSGQQKPHPGERLKTGLLSRSPVCSCESASPCPKQSPRVAKTQQKRRNCSSAEDFDHHGRVSLGSDRLVPREIIVEKSKAVRVLPASELSDPGLLLKQDLAKTTSKEELHVLESLSSRHLMKNNPGQAQQTGLATNTERLSTIQNSPTKKRKKYERGH

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	DNA repair endonuclease XPF
Molecular weight formula_weight	106894.5 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MGSSHHHHHHENLYFQSNAMESGQPARRIAMAPLLEYERQLVLELLDTDGLVVCARGLGADRLLYHFLQLHCHPACLVLVLNTQPAEEEYFINQLKIEGVEHLPRRVTNEITSNSRYEVYTQGGVIFATSRILVVDFLTDRIPSDLITGILVYRAHRIIESCQEAFILRLFRQKNKRGFIKAFTDNAVAFDTGFCHVERVMRNLFVRKLYLWPRFHVAVNSFLEQHKPEVVEIHVSMTPTMLAIQTAILDILNACLKELKCHNPSLEVEDLSLENAIGKPFDKTIRHYLDPLWHQLGAKTKSLVQDLKILRTLLQYLSQYDCVTFLNLLESLRATEKAFGQNSGWLFLDSSTSMFINARARVYHLPDAKMSKKEKISEKMEIKEGEETKKELVLESNPKWEALTEVLKEIEAENKESEALGGPGQVLICASDDRTCSQLRDYITLGAEAFLLRLYRKTFEKDSKAEEVWMKFRKEDSSKRIRKSHKRPKDPQNKERASTKERTLKKKKRKLTLTQMVGKPEELEEEGDVEEGYRREISSSPESCPEEIKHEEFDVNLSSDAAFGILKEPLTIIHPLLGCSDPYALTRVLHEVEPRYVVLYDAELTFVRQLEIYRASRPGKPLRVYFLIYGGSTEEQRYLTALRKEKEAFEKLIREKASMVVPEEREGRDETNLDLVRGTASADVSTDTRKAGGQEQNGTQQSIVVDMREFRSELPSLIHRRGIDIEPVTLEVGDYILTPEMCVERKSISDLIGSLNNGRLYSQCISMSRYYKRPVLLIEFDPSKPFSLTSRGALFQEISSNDISSKLTLLTLHFPRLRILWCPSPHATAELFEELKQSKPQPDAATALAITADSETLPESEKYNPGPQDFLLKMPGVNAKNCRSLMHHVKNIAELAALSQDELTSILGNAANAKQLYDFIHTSFAEVVSKGKGKK

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	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	DNA excision repair protein ERCC-1
Molecular weight formula_weight	32598.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP

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	Spodoptera frugiperda

Entity 4 Entity 4 polymer

Description description	Structure-specific endonuclease subunit SLX4
Molecular weight formula_weight	29617.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MASWSHPQFEKGGGSGGGSGGGSWSHPQFEKSGGGSENLYFQSNAVPQIPECPICGKPFLTLKSRTSHLKQCAVKMEVGPQLLLQAVRLQTAQPEGSSSPPMFSFSDHSRGLKRRGPTSKKEPRKRRKVDEAPSEDLLVAMALSRSEMEPGAAVPALRLESAFSERIRPEAENKSRKKKPPVSPPLLLVQDSETTGRQIEDRVALLLSEEVELSSTPPLPASRILKEGWERAGQCPPPPERKQSFLWEGSALTGAWAMEDFYTARLVPPLV

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	Spodoptera frugiperda

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	22617

fit	/app/data/saxs_computation/qe/9qed/9qed.fit
pddf	/app/data/pr_computation/qe/9qed/9qed.pr.out
profile	/app/data/saxs_computation/qe/9qed/9qed.dat

Cryo-EM structure of the XPF-ERCC1-SLX4(330-555)-SLX4IP complex

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

Protein SLX4IP

State in the Current Structure

Other States of the Same Protein in the Database

DNA repair endonuclease XPF

State in the Current Structure

Other States of the Same Protein in the Database

DNA excision repair protein ERCC-1

State in the Current Structure

Other States of the Same Protein in the Database

Structure-specific endonuclease subunit SLX4

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)