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- PDB-10aj: Crystal Structure of Human WRN helicase with compound 1 -

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Basic information

Entry
Database: PDB / ID: 10aj
TitleCrystal Structure of Human WRN helicase with compound 1
ComponentsBifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / DNA helicase / RecQ family / allosteric inhibitor / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of strand invasion / 3'-flap-structured DNA binding / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / DNA geometric change / telomere maintenance via semi-conservative replication / four-way junction helicase activity / Y-form DNA binding ...positive regulation of strand invasion / 3'-flap-structured DNA binding / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / DNA geometric change / telomere maintenance via semi-conservative replication / four-way junction helicase activity / Y-form DNA binding / telomeric D-loop disassembly / t-circle formation / G-quadruplex DNA binding / bubble DNA binding / exonuclease activity / MutLalpha complex binding / Impaired BRCA2 binding to PALB2 / protein localization to nucleolus / response to UV-C / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / DNA metabolic process / DNA synthesis involved in DNA repair / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / HDR through Single Strand Annealing (SSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / Impaired BRCA2 binding to RAD51 / DNA 3'-5' helicase / Presynaptic phase of homologous DNA pairing and strand exchange / 3'-5' DNA helicase activity / mismatch repair / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / 3'-5' exonuclease activity / telomere maintenance / replication fork processing / cellular response to starvation / replication fork / cellular response to gamma radiation / base-excision repair / G2/M DNA damage checkpoint / cellular senescence / HDR through Homologous Recombination (HRR) / double-strand break repair / manganese ion binding / DNA recombination / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / Hydrolases; Acting on ester bonds / DNA helicase activity / chromosome, telomeric region / nuclear speck / chromosome / centrosome / DNA damage response / nucleolus / protein-containing complex binding / magnesium ion binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / HRDC domain / HRDC domain ...Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / HRDC domain / HRDC domain / DNA helicase, ATP-dependent, RecQ type / HRDC domain profile. / HRDC domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / HRDC-like superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsToms, A.V. / Caravella, J.A. / Sitnikov, N. / Bartels, F. / Svensson, R. / Jacques O'Hagan, S. / Borthwick, J. / Campos, S. / Yin, Y. / Zhao, X. ...Toms, A.V. / Caravella, J.A. / Sitnikov, N. / Bartels, F. / Svensson, R. / Jacques O'Hagan, S. / Borthwick, J. / Campos, S. / Yin, Y. / Zhao, X. / Li, L. / Talbot, E. / Kong, H. / Freund, R.R.A. / Browning, B. / Genung, N.E. / Carreiro, S. / Brennan, D. / Graves, A.P. / Loh, C. / Tummino, P. / Edmonson, S.E. / Li, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2026
Title: Design of Cyclic Vinyl Sulfones as WRN Covalent Inhibitors from Noncovalent Binders.
Authors: Caravella, J.A. / Toms, A.V. / Sitnikov, N. / Bartels, F. / Svensson, R. / O'Hagan, S.J. / Borthwick, J.A. / Campos, S. / Yin, Y. / Zhao, X. / Li, L. / Liu, R. / Talbot, E. / Kong, H. / ...Authors: Caravella, J.A. / Toms, A.V. / Sitnikov, N. / Bartels, F. / Svensson, R. / O'Hagan, S.J. / Borthwick, J.A. / Campos, S. / Yin, Y. / Zhao, X. / Li, L. / Liu, R. / Talbot, E. / Kong, H. / Adolf Freund, R.R. / Browning, B. / Genung, N.E. / Carreiro, S. / Brennan, D. / Graves, A.P. / Loh, C. / Tummino, P. / Edmondson, S.D. / Li, D.
History
DepositionJan 8, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4204
Polymers48,9211
Non-polymers4993
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.130, 58.180, 131.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN / DNA helicase / RecQ-like type 3 / RecQ protein-like 2 / Werner syndrome protein


Mass: 48921.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WRN, RECQ3, RECQL2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q14191, Hydrolases; Acting on ester bonds, DNA 3'-5' helicase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1C4J / 4-(4-methyl-4H-1,2,4-triazol-3-yl)-1-[4-(1H-pyrrol-1-yl)benzene-1-sulfonyl]piperidine


Mass: 371.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21N5O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: protocol was established using PROTEROS Standard Protocols

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→65.94 Å / Num. obs: 17771 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.027 / Rsym value: 0.073 / Net I/σ(I): 15.3
Reflection shellResolution: 2.42→2.46 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.55 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 870 / CC1/2: 0.628 / Rsym value: 1.45 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
REFMACv5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→65.94 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.254 860 5 %Random
Rwork0.211 ---
obs-16911 100 %-
Refinement stepCycle: LAST / Resolution: 2.42→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3355 0 31 31 3417

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