3aaf

Structure of WRN RQC domain bound to double-stranded DNA

Method: X-RAY DIFFRACTION D_max: 87.6 Å Quality: GOOD

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

Werner syndrome ATP-dependent helicase

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 949–1079 Chain B； UniProt 949–1079	Fragment：RecQ C-terminal (RQC) domain	;DNA (5'-D(APCPCPCPTPAPAPTPTPAPGPGPGPT)-3') ; × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 9；293 K；20% PEG 4000, 0.2M sodium acetate, 0.1M CAPS-NaOH, pH 9, VAPOR DIFFUSION, temperature 293K	Resolution 1.90 Å R-free 0.244

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 3AAF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10AJ Crystal Structure of Human WRN helicase with compound 1 Deposited 2026-01-08	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 518–946（429 aa）	Not recorded	ZN ZINC ION × 1 A1C4J 4-(4-methyl-4H-1,2,4-triazol-3-yl)-1-[4-(1H-pyrrol-1-yl)benzene-1-sulfonyl]piperidine × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；290 K；protocol was established using PROTEROS Standard Protocols	Resolution 2.42 Å R-free 0.254
10AK Crystal Structure of Human WRN helicase with compound 4 Deposited 2026-01-08	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 516–946（431 aa）	Not recorded	ZN ZINC ION × 1 A1C4L N-benzyl-N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-2-[4-(1H-pyrrol-1-yl)phenyl]acetamide × 1 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；290 K；protocol was established using PROTEROS Standard Protocols	Resolution 1.37 Å R-free 0.214
10AP Crystal Structure of Human WRN helicase with compound 26 Deposited 2026-01-08	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 500–946（447 aa）	Not recorded	A1C4O (2R)-N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N-{[2-(2-hydroxypropan-2-yl)pyridin-4-yl]methyl}-2-methoxy-2-[(1M)-3,3',4'-trifluoro[1,1'-biphenyl]-4-yl]acetamide × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；co-crystallization additive 46 [Proplex-E2-B4+29% glycerol]	Resolution 2.58 Å R-free 0.286
2AXL Solution structure of a multifunctional DNA- and protein-binding domain of human Werner syndrome protein Deposited 2005-09-05	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 949–1092（144 aa） Fragment：The DPBD	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；295.2 K；Ionic strength (raw mmCIF value) 25 mM KPi + 25 mM NaCl；Pressure 1 NMR sample composition 0.35 mM in KPi buffer (pH7.4) 25 mM NaCl \| 92.5% H2O/7.5% D2O	Resolution not provided
2DGZ Solution structure of the Helicase and RNase D C-terminal domain in Werner syndrome ATP-dependent helicase Deposited 2006-03-16	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 1140–1239（100 aa） Fragment：Helicase and RNase D C-terminal domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient NMR sample composition 20mM d-Tris-HCl(pH7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2E1E Crystal structure of the HRDC Domain of Human Werner Syndrome Protein, WRN Deposited 2006-10-25	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 1142–1242（101 aa） Fragment：HRDC domain	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9.5；293 K；pH 9.5, VAPOR DIFFUSION, temperature 293K	Resolution 2.30 Å R-free 0.279
2E1E Crystal structure of the HRDC Domain of Human Werner Syndrome Protein, WRN Deposited 2006-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1142–1242（101 aa） Fragment：HRDC domain	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9.5；293 K；pH 9.5, VAPOR DIFFUSION, temperature 293K	Resolution 2.30 Å R-free 0.279
2E1F Crystal structure of the HRDC Domain of Human Werner Syndrome Protein, WRN Deposited 2006-10-25	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 1142–1242（101 aa） Fragment：HRDC domain	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；pH 5.5, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.255
2E1F Crystal structure of the HRDC Domain of Human Werner Syndrome Protein, WRN Deposited 2006-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1142–1242（101 aa） Fragment：HRDC domain	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；pH 5.5, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.255
2FBT WRN exonuclease Deposited 2005-12-10	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 38–236（199 aa） Fragment：Exonculease domain	Not recorded	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；277 K；5ul of 4.5mg/ml WRN exonuclease buffered in 25mM Tris HCl, 100mM NaCl, pH7.5, mixed with 5ul 1% MPEG 2K, 200mM Na Acetate, pH 4.5 from the reservoir solution and 1ul EDTA additive. , VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 4.50	Resolution 2.05 Å R-free 0.241
2FBV WRN exonuclease, Mn complex Deposited 2005-12-10	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 38–236（199 aa） Fragment：Exonuclease domain	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；277 K；5ul of 4.5mg/ml WRN exonuclease buffered in 25mM Tris HCL, 100mM NaCl, pH7.5, mixed with 5ul 1% MPEG 2K, 200mM Na Acetate, pH 4.5 from the reservior solution and 1ul EDTA additive, pH 4.50, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.40 Å R-free 0.277
2FBX WRN exonuclease, Mg complex Deposited 2005-12-10	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 38–236（199 aa） Fragment：Exonuclease domain	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；5ul of 4.5mg/ml WRN exonuclease buffered in 25mM Tris HCL, 100mM NaCl, pH 7.5, mixed with 5ul 1% MPEG 2K, 200mM Na Acetate, pH 4.5 from the reservior solution and 1ul EDTA additive, pH 4.50, VAPOR DIFFUSION, SITTING DROP	Resolution 2.20 Å R-free 0.262
2FBY WRN exonuclease, Eu complex Deposited 2005-12-10	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 38–236（199 aa） Fragment：Exonuclease domain	Not recorded	EU3 EUROPIUM (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；5ul of 4.5mg/ml WRN exonuclease buffered in 25mM Tris HCL, 100mM NaCl, pH 7.5, mixed with 5ul 1% MPEG 2K, 200mM Na Acetate, pH 4.5 from the reservior solution and 1ul EDTA additive, VAPOR DIFFUSION, SITTING DROP, pH 4.50	Resolution 2.00 Å R-free 0.245
2FC0 WRN exonuclease, Mn dGMP complex Deposited 2005-12-10	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 38–236（199 aa） Fragment：Exonuclease domain	Not recorded	MN MANGANESE (II) ION × 2 DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；277 K；5ul of 4.5mg/ml WRN exonuclease buffered in 25mM Tris HCl, 100mM NaCl, pH 7.5, mixed with 5ul 1% MPEG 2K, 200mM Na Acetate, pH 4.5 from the reservior solution and 1ul EDTA additive, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 4.50	Resolution 2.00 Å R-free 0.238
6YHR Crystal structure of Werner syndrome helicase Deposited 2020-03-30	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 517–1094（578 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1M Na Acetate, 0.1 M Cacodylate pH 6.5	Resolution 2.20 Å R-free 0.236
7GQS Crystal Structure of Werner helicase fragment 517-945 in complex with ADP Deposited 2023-10-19	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 517–945（429 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 CD CADMIUM ION × 3 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；5 mg/mL protein in 20mM TRIS/HCl pH7.5, 350mM NaCl, 0.25mM TCEP, 2.5% glycerol mixed 40nL with 180nL reservoir consisting of 9.091 %w/v Silver Bullets 42, 0.091 M MES monohydrate, 2.727 %v/v Jeffamine T-403, 13.6 %v/v pentaerythritol ethoxylate, 0.182M Potassium acetate pH6	Resolution 1.57 Å R-free 0.218
7GQT Crystal Structure of Werner helicase fragment 517-945 in complex with ATP Deposited 2023-10-19	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 517–945（429 aa）	Not recorded	ZN ZINC ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；277 K；5 mg/mL protein in 20mM TRIS/HCl pH7.5, 350mM NaCl, 0.25mM TCEP, 2.5% glycerol mixed 20nL with 20nL seed solution and 110nL reservoir consisting of 0.2M NaCl, 0.1M Na/K Phosphate, 10%w/v PEG8000	Resolution 2.21 Å R-free 0.263
7GQU Crystal Structure of Werner helicase fragment 517-945 in covalent complex with N-[(E,1S)-1-cyclopropyl-3-methylsulfonylprop-2-enyl]-2-(1,1-difluoroethyl)-4-phenoxypyrimidine-5-carboxamide Deposited 2023-10-19	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 517–945（429 aa）	Not recorded	ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X1L N-[(1S)-1-cyclopropyl-3-(methanesulfonyl)propyl]-2-(1,1-difluoroethyl)-4-phenoxypyrimidine-5-carboxamide × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；5 mg/mL protein in 20mM TRIS/HCl pH7.5, 350mM NaCl, 0.25mM TCEP, 2.5% glycerol mixed 40nL with 180nL reservoir consisting of 20 %v/v Ethylene glycol, 11 %w/v PEG8000, 0.08M MES/NaOH pH6.2, 0.08M imidazole	Resolution 1.54 Å R-free 0.209
7XUT Crystal structure of RPA70N-WRN fusion Deposited 2022-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 435–451（17 aa） Chain B 435–451（17 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；20% PEG3350, 200 mM ammonium sulfate	Resolution 1.60 Å R-free 0.214
8PFL Crystal structure of WRN helicase domain in complex with 3 Deposited 2023-06-16	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 517–945（429 aa）	Mutation：E625A, R564A, R785A, R803A, E886A, R942A	ZN ZINC ION × 1 YH8 2-[2-(3,6-dihydro-2~{H}-pyran-4-yl)-5-ethyl-7-oxidanylidene-6-[4-(3-oxidanylpyridin-2-yl)carbonylpiperazin-1-yl]-[1,2,4]triazolo[1,5-a]pyrimidin-4-yl]-~{N}-[2-methyl-4-(trifluoromethyl)phenyl]ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% Jeffamine ED-2001 0.1 M Hepes pH 7	Resolution 1.80 Å R-free 0.226
8PFO Crystal structure of WRN helicase domain in complex with HRO761 Deposited 2023-06-16	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 517–945（429 aa）	Mutation：E625A, R564A, R785A, R803A, E886A, R942A	ZN ZINC ION × 1 YHC ~{N}-[2-chloranyl-4-(trifluoromethyl)phenyl]-2-[2-(3,6-dihydro-2~{H}-pyran-4-yl)-5-ethyl-6-[4-(6-methyl-5-oxidanyl-pyrimidin-4-yl)carbonylpiperazin-1-yl]-7-oxidanylidene-[1,2,4]triazolo[1,5-a]pyrimidin-4-yl]ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25.5 % PEG 4000 0.17 M ammonium sulfate 15 % glycerol	Resolution 1.90 Å R-free 0.248
8PFP Crystal structure of WRN helicase domain in complex with ATPgammaS Deposited 2023-06-16	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 517–945（429 aa）	Mutation：E625A, R716A, K804A, E886A, R942A	ZN ZINC ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 % PEG3350 0.2 M Sodium citrate tribasic dihydrate	Resolution 1.60 Å R-free 0.238
8YLE Crystal structure of Werner syndrome helicase complexed with AMP-PCP Deposited 2024-03-06	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 517–945（429 aa）	Not recorded	ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；pH 6.5,0.1 M Amino acids,0.1 M Buffer System 1, 30.00% % v/v EDO_P8K	Resolution 1.86 Å R-free 0.214
9HZG Ku70/80 bound to WRN-exo Deposited 2025-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain E 1–1432（1432 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9MJS Crystal structure of WRN helicase with bound AMPPNP Deposited 2024-12-16	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；30% Jeffamine ED 2003, 0.2 M NaCl, 0.2 M NDSB-201, 0.1 M MES	Resolution 1.84 Å R-free 0.225
9MJS Crystal structure of WRN helicase with bound AMPPNP Deposited 2024-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；30% Jeffamine ED 2003, 0.2 M NaCl, 0.2 M NDSB-201, 0.1 M MES	Resolution 1.84 Å R-free 0.225
9MJT Crystal structure of apo WRN helicase in Form D Deposited 2024-12-16	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；21-27.5% w/v PEG1500, 0.1 M MMT, pH 5.75-6.25	Resolution 1.73 Å R-free 0.259
9MJU Crystal structure of WRN helicase with allosteric fragment 1 Deposited 2024-12-16	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1BL1 N-[4-(trifluoromethyl)phenyl]acetamide × 1 EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20% v/v PEG6000, 0.1 M HEPES, pH 6.25-6.5	Resolution 1.58 Å R-free 0.243
9MJV Crystal structure of WRN helicase with bound allosteric fragment 2 Deposited 2024-12-16	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1BL2 2-[4-(trifluoromethoxy)phenyl]-2H-tetrazole-5-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；21-27.5% w/v PEG1500, 0.1 M MMT, pH 5.75-6.25	Resolution 2.58 Å R-free 0.288
9MJW Crystal structure of WRN helicase with bound allosteric fragment 3. Deposited 2024-12-16	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1BL3 6-chloro-7-methyl-1lambda~6~,2,4-benzothiadiazine-1,1,3(2H,4H)-trione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；21%-27.5% (w/v) PEG 1500 and 0.1 M MMT pH 5.75-6.25	Resolution 2.00 Å R-free 0.263
9MJX Crystal structure of WRN helicase with bound allosteric fragment 4 Deposited 2024-12-16	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1BL4 (4R)-8-amino-2-cyclopropylimidazo[1,2-a]pyridine-6-carboxylic acid × 1 A1BL5 5,6-diaminopyridine-3-carboxylic acid × 1 SO4 SULFATE ION × 2 CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；21%-27.5% (w/v) PEG 1500 and 0.1 M MMT pH 5.75-6.25	Resolution 1.73 Å R-free 0.229
9MJY Crystal structure of WRN helicase with bound allosteric compound 1 Deposited 2024-12-16	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1BL0 (3-{[4-(trifluoromethyl)phenyl]carbamoyl}furan-2-yl)acetic acid × 2 CL CHLORIDE ION × 5 EDO 1,2-ETHANEDIOL × 5 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；21%-27.5% (w/v) PEG 1500 and 0.1 M MMT pH 5.75-6.25	Resolution 1.63 Å R-free 0.222
9MJZ Crystal structure of WRN helicase with bound allosteric compound 3 Deposited 2024-12-16	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1BL6 (2-anilino-5-{[4-(trifluoromethyl)phenyl]carbamoyl}-1,3-thiazol-4-yl)acetic acid × 1 EDO 1,2-ETHANEDIOL × 8 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；21-27.5% w/v PEG1500, 0.1 M MMT, pH 5.75-6.25	Resolution 1.70 Å R-free 0.261
9MK0 Crystal structure of WRN helicase with bound allosteric compound 5 Deposited 2024-12-16	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 500–942（443 aa）	Not recorded	ZN ZINC ION × 1 A1BL7 (2-[4-(pyrimidine-4-carbonyl)piperazin-1-yl]-4-{[4-(trifluoromethyl)phenyl]carbamoyl}pyrimidin-5-yl)acetic acid × 1 EDO 1,2-ETHANEDIOL × 12 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% w/v PEG6000, 0.2 M calcium chloride, 0.1 M MES, pH 6.0	Resolution 1.89 Å R-free 0.230
9MK1 Crystal structure of WRN helicase with bound compound 6 Deposited 2024-12-16	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1BL8 (2-[(2R)-2-(phenylcarbamoyl)-2,3-dihydro-1H-inden-4-yl]-5-{[4-(trifluoromethyl)phenyl]carbamoyl}-1,3-thiazol-4-yl)acetic acid × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；24.5% w/v PEG1500, 0.1 M MMT, pH 6.0	Resolution 2.12 Å R-free 0.267
9OG3 Crystal structure of WRN in complex with compound 4 Deposited 2025-04-30	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 526–946（421 aa）	Not recorded	A1CA4 (3R,4S)-N-[(2R)-3-cyclohexyl-1-(dimethylamino)-1-oxopropan-2-yl]-1-[(2-fluoro-4-methylphenyl)acetyl]-4-[3-(2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)propanamido]piperidine-3-carboxamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290.15 K；18% w/v PEG3350 and 0.18 M Tri-sodium citrate	Resolution 2.06 Å R-free 0.258
9OG8 Crystal structure of WRN in complex with compound 43 Deposited 2025-04-30	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 526–946（421 aa）	Not recorded	A1CA5 (3R,4S)-N-[(2R)-3-cyclohexyl-1-(methylamino)-1-oxopropan-2-yl]-4-{3-[6-(ethanesulfonamido)-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl]propanamido}-1-[(2-fluoro-4-methylphenyl)acetyl]piperidine-3-carboxamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290.15 K；18.0% w/v PEG 3350, 0.18 M Tri-ammonium citrate	Resolution 1.66 Å R-free 0.239
9OW9 Human WRN helicase in complex with allosteric ligand Compound 1 Deposited 2025-06-02	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1CEV 2-[(9R)-1'-[(1,3-benzoxazol-2-yl)acetyl]-2-(morpholin-4-yl)-8-oxo-5,8-dihydro-4H-spiro[furo[3,4-d][1,2,4]triazolo[1,5-a]pyrimidine-7,4'-piperidin]-4-yl]-N-[2-chloro-4-(trifluoromethyl)phenyl]acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；23-24.5% w/v PEG1500, 100 mM MMT, pH 5.75-6.25	Resolution 2.34 Å R-free 0.301
9OWA Human WRN helicase in complex with allosteric ligand Compound 2 Deposited 2025-06-02	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1CEW N-[2-chloro-4-(trifluoromethyl)phenyl]-2-[(5'R,10'R)-2'-(3,6-dihydro-2H-pyran-4-yl)-1-(5-hydroxy-6-methylpyrimidine-4-carbonyl)-5'-methyl-9'-oxo-5',9'-dihydrospiro[piperidine-4,8'-pyrano[4,3-d][1,2,4]triazolo[1,5-a]pyrimidin]-4'(6'H)-yl]acetamide × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；23-24.5% w/v PEG1500, 100 mM MMT, pH 5.75-6.25	Resolution 1.98 Å R-free 0.306
9OWB Human WRN helicase in complex with allosteric ligand Compound 6 Deposited 2025-06-02	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1CEX N-[2-chloro-4-(trifluoromethyl)phenyl]-2-[(10'R)-1-(3-hydroxypyridine-2-carbonyl)-2'-(morpholin-4-yl)-9'-oxo-5',9'-dihydrospiro[piperidine-4,8'-pyrano[4,3-d][1,2,4]triazolo[1,5-a]pyrimidin]-4'(6'H)-yl]acetamide × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20.0% w/v PEG3350, 200 mM ammonium tartrate	Resolution 1.56 Å R-free 0.192
9OWB Human WRN helicase in complex with allosteric ligand Compound 6 Deposited 2025-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1CEX N-[2-chloro-4-(trifluoromethyl)phenyl]-2-[(10'R)-1-(3-hydroxypyridine-2-carbonyl)-2'-(morpholin-4-yl)-9'-oxo-5',9'-dihydrospiro[piperidine-4,8'-pyrano[4,3-d][1,2,4]triazolo[1,5-a]pyrimidin]-4'(6'H)-yl]acetamide × 1 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20.0% w/v PEG3350, 200 mM ammonium tartrate	Resolution 1.56 Å R-free 0.192
9OWB Human WRN helicase in complex with allosteric ligand Compound 6 Deposited 2025-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1CEX N-[2-chloro-4-(trifluoromethyl)phenyl]-2-[(10'R)-1-(3-hydroxypyridine-2-carbonyl)-2'-(morpholin-4-yl)-9'-oxo-5',9'-dihydrospiro[piperidine-4,8'-pyrano[4,3-d][1,2,4]triazolo[1,5-a]pyrimidin]-4'(6'H)-yl]acetamide × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20.0% w/v PEG3350, 200 mM ammonium tartrate	Resolution 1.56 Å R-free 0.192
9OWB Human WRN helicase in complex with allosteric ligand Compound 6 Deposited 2025-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1CEX N-[2-chloro-4-(trifluoromethyl)phenyl]-2-[(10'R)-1-(3-hydroxypyridine-2-carbonyl)-2'-(morpholin-4-yl)-9'-oxo-5',9'-dihydrospiro[piperidine-4,8'-pyrano[4,3-d][1,2,4]triazolo[1,5-a]pyrimidin]-4'(6'H)-yl]acetamide × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20.0% w/v PEG3350, 200 mM ammonium tartrate	Resolution 1.56 Å R-free 0.192
9OWC Human WRN helicase in complex with allosteric ligand Compound 7 Deposited 2025-06-02	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1CEY N-[2-chloro-4-(trifluoromethyl)phenyl]-2-[(5S,9R)-1'-(3-hydroxypyridine-2-carbonyl)-5-methyl-2-(morpholin-4-yl)-8-oxo-5,8-dihydrospiro[cyclopenta[d][1,2,4]triazolo[1,5-a]pyrimidine-7,4'-piperidin]-4(6H)-yl]acetamide × 1 EDO 1,2-ETHANEDIOL × 8 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；23-24.5% w/v PEG1500, 100 mM MMT, pH 5.75-6.25	Resolution 1.67 Å R-free 0.206
9OWD Human WRN helicase in complex with allosteric ligand Compound 9 Deposited 2025-06-02	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 500–942（443 aa） Fragment：UNP residues 500-942	Not recorded	ZN ZINC ION × 1 A1CEZ N-[2-chloro-4-(trifluoromethyl)phenyl]-2-[(9R)-1'-(5-hydroxy-6-methylpyrimidine-4-carbonyl)-2-(morpholin-4-yl)-8-oxo-5,8-dihydrospiro[cyclopenta[d][1,2,4]triazolo[1,5-a]pyrimidine-7,4'-piperidin]-4(6H)-yl]acetamide × 1 EDO 1,2-ETHANEDIOL × 5 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；23-24.5% w/v PEG1500, 100 mM MMT, pH 5.75-6.25	Resolution 1.96 Å R-free 0.272
9QBU Crystal structure of WRN in complex with (S)-27 (GSK5819992) Deposited 2025-03-03	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 500–942（443 aa）	Not recorded	A1I5L 1-[(2~{S})-2-(2-azaspiro[3.3]heptan-2-ylcarbonyl)-4-[2-[4-(trifluoromethyl)phenyl]ethanoyl]piperazin-1-yl]propan-1-one × 1 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；7% PEG 20000, 0.1 M MES pH 5.5	Resolution 2.10 Å R-free 0.249
9QBU Crystal structure of WRN in complex with (S)-27 (GSK5819992) Deposited 2025-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 500–942（443 aa）	Not recorded	A1I5L 1-[(2~{S})-2-(2-azaspiro[3.3]heptan-2-ylcarbonyl)-4-[2-[4-(trifluoromethyl)phenyl]ethanoyl]piperazin-1-yl]propan-1-one × 1 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；7% PEG 20000, 0.1 M MES pH 5.5	Resolution 2.10 Å R-free 0.249
9QBV Crystal structure of WRN in complex with (R)-11 (GSK4766470) Deposited 2025-03-03	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 500–942（443 aa）	Not recorded	A1I5F 1-[(2~{R})-2-methyl-4-[2-[4-(trifluoromethyl)phenyl]ethanoyl]piperazin-1-yl]propan-1-one × 1 EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；10% PEG 6000, 0.1 M HEPES pH 7.0	Resolution 2.15 Å R-free 0.258
9RTI Structure of WRN in complex with ATPgS and covalent ligand Compound 7 Deposited 2025-07-02	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 517–941（425 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 15 A1JJ8 ~{N}-[1-[(4-fluorophenyl)methyl]-7-methyl-indazol-3-yl]propanamide × 1 A1JJQ ~{N}-[1-[(4-fluorophenyl)methyl]-7-methyl-indazol-3-yl]prop-2-enamide × 1 MLT D-MALATE × 1 PEG DI(HYDROXYETHYL)ETHER × 5 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；100 mM MMT pH 7.2, 25% w/v PEG 1500, 20% EG	Resolution 2.20 Å R-free 0.274
9RUR Structure of WRN in complex with ATPgS and covalent ligand Compound 4d Deposited 2025-07-04	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 517–941（425 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 DMS DIMETHYL SULFOXIDE × 3 EDO 1,2-ETHANEDIOL × 4 A1JJK 2-ethylsulfanyl-~{N}-[1-[(4-fluorophenyl)methyl]indazol-3-yl]ethanamide × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；0.1 mM MMT pH 7.2, 25 %w/v PEG 1500 and 20 %v/v EG	Resolution 2.30 Å R-free 0.281
9RUR Structure of WRN in complex with ATPgS and covalent ligand Compound 4d Deposited 2025-07-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 517–941（425 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 4 ZN ZINC ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；0.1 mM MMT pH 7.2, 25 %w/v PEG 1500 and 20 %v/v EG	Resolution 2.30 Å R-free 0.281
9RUS Structure of WRN in complex with ATPgS and Compound 3 Deposited 2025-07-04	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 517–941（425 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 GQP 1-[(4-fluorophenyl)methyl]benzimidazole × 1 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；0.1 mM MMT pH 7.2, 25 %w/v PEG 1500	Resolution 2.19 Å R-free 0.298
9RUS Structure of WRN in complex with ATPgS and Compound 3 Deposited 2025-07-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 517–941（425 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；0.1 mM MMT pH 7.2, 25 %w/v PEG 1500	Resolution 2.19 Å R-free 0.298
9S17 WRN helicase in complex with molecule 81 Deposited 2025-07-18	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 517–941（425 aa）	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5 A1JKV (2~{R},4~{R})-4-ethyl-~{N}-[(2~{S})-4-methylsulfonylbutan-2-yl]-2-phenyl-piperidine-1-carboxamide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；100 mM BIS-TRIS 5.8 pH, 26 % w/v PEG 3350 and 275 mM LiSO4	Resolution 1.91 Å R-free 0.248
9S17 WRN helicase in complex with molecule 81 Deposited 2025-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 517–941（425 aa）	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 12 A1JKV (2~{R},4~{R})-4-ethyl-~{N}-[(2~{S})-4-methylsulfonylbutan-2-yl]-2-phenyl-piperidine-1-carboxamide × 1 SO4 SULFATE ION × 4 DMS DIMETHYL SULFOXIDE × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；100 mM BIS-TRIS 5.8 pH, 26 % w/v PEG 3350 and 275 mM LiSO4	Resolution 1.91 Å R-free 0.248
9S18 WRN helicase in complex with HRO761 Deposited 2025-07-18	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 517–943（427 aa）	Not recorded	FLC CITRATE ANION × 3 EDO 1,2-ETHANEDIOL × 4 YHC ~{N}-[2-chloranyl-4-(trifluoromethyl)phenyl]-2-[2-(3,6-dihydro-2~{H}-pyran-4-yl)-5-ethyl-6-[4-(6-methyl-5-oxidanyl-pyrimidin-4-yl)carbonylpiperazin-1-yl]-7-oxidanylidene-[1,2,4]triazolo[1,5-a]pyrimidin-4-yl]ethanamide × 1 DMS DIMETHYL SULFOXIDE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；0.3M trisodium citrate tetrahydrate, 0.1M sodium citrate, pH 4.25 and 10% PEG 3350.	Resolution 2.00 Å R-free 0.251
9S19 WRN helicase in complex with ATPgS and ssDNA Deposited 2025-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 517–941（425 aa）	Not recorded	ZN ZINC ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 EDO 1,2-ETHANEDIOL × 6 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100mM HEPES pH 7.2 and 15% w/v PEG 8K	Resolution 2.30 Å R-free 0.257
9S19 WRN helicase in complex with ATPgS and ssDNA Deposited 2025-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 517–941（425 aa）	Not recorded	ZN ZINC ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 EDO 1,2-ETHANEDIOL × 5 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100mM HEPES pH 7.2 and 15% w/v PEG 8K	Resolution 2.30 Å R-free 0.257
9S1A WRN helicase in the absence of nucleotide or DNA Deposited 2025-07-18	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 517–941（425 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；100mM BIS-TRIS pH 5.8, 25% w/v PEG3350 and 200mM LiSO4.	Resolution 1.96 Å R-free 0.247
9S1A WRN helicase in the absence of nucleotide or DNA Deposited 2025-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 517–941（425 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 6 DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；100mM BIS-TRIS pH 5.8, 25% w/v PEG3350 and 200mM LiSO4.	Resolution 1.96 Å R-free 0.247
9S1B WRN helicase in complex with covalent inhibitor GSK_WRN3 Deposited 2025-07-18	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 517–943（427 aa）	Not recorded	ZN ZINC ION × 1 A1JKU ~{N}-[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]-5-oxidanyl-2-oxidanylidene-6-phenyl-1~{H}-pyridine-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；0.3M trisodium citrate tetrahydrate, 0.1M sodium citrate, pH 4.25 and 10% PEG 3350	Resolution 2.22 Å R-free 0.294

49 other PDB entries and 61 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	WRN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–134； UniProt 949–1079 Author chain B； PDBConstruct 4–134； UniProt 949–1079

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3aaf
Deposition date deposition_date	2009-11-16
Structure title title	Structure of WRN RQC domain bound to double-stranded DNA
Keywords keywords	HELIX-TURN-HELIX, WINGED-HELIX, PROTEIN-DNA COMPLEX, DNA-binding, Helicase, 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	24.08 Å
Radius of gyration Rg (electron density) rg_electron	24.80 Å
Forward intensity I(0) i0	24949600.00
Molecular weight molecular_weight	33753.0 kDa
Excluded volume excluded_volume	40240 Å³
Envelope volume envelope_volume	52410 Å³
Hydration-shell volume shell_volume	18874 Å³
Envelope diameter envelope_diameter	89.1 Å
Shell Rg shell_rg	30.10 Å
Envelope Rg envelope_rg	24.74 Å
Shape Rg shape_rg	24.86 Å
Total Rg total_rg	25.23 Å
Total atoms total_atoms	2352
Residues n_residues	246
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	87.6 Å
Rg (real space) rg_real	24.30 Å
Rg uncertainty (real space) rg_real_error	0.84 Å
I(0) (real space) i0_real	2.4950e+07
I(0) uncertainty (real space) i0_real_error	3.4050e+05
Rg (reciprocal space) rg_reciprocal	24.25 Å
I(0) (reciprocal space) i0_reciprocal	24950000.0000
Solution quality estimate total_estimate	0.8156
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.560
Kurtosis Kurtosis kurtosis	-0.121
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3392000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.655; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.642; Smooth: 0.992

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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	Werner syndrome ATP-dependent helicase
Molecular weight formula_weight	15351.5 kDa
EC 编号 ec_number	3.6.1.-
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	2690

GIRMDDSEDTSWDFGPQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLADQYRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEVSRYNKFMKICALTKKGRNWLHKANTESQSLILQANEELCPKKFLLPSS

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(APCPCPCPTPAPAPTPTPAPGPGPGPT)-3') ;
Molecular weight formula_weight	4279.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D

ACCCTAATTAGGGT

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	338

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3aafA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	3aafB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	84.077 Å
Unit-cell length b length_b	84.077 Å
Unit-cell length c length_c	145.291 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	16

Space group space_group	P 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2134
R_work r_work	0.2118
R_free r_free	0.2435

fit	/app/data/saxs_computation/aa/3aaf/3aaf.fit
pddf	/app/data/pr_computation/aa/3aaf/3aaf.pr.out
profile	/app/data/saxs_computation/aa/3aaf/3aaf.dat

Structure of WRN RQC domain bound to double-stranded DNA

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

Werner syndrome ATP-dependent helicase

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 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)