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- PDB-9mjw: Crystal structure of WRN helicase with bound allosteric fragment 3. -

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Basic information

Entry
Database: PDB / ID: 9mjw
TitleCrystal structure of WRN helicase with bound allosteric fragment 3.
ComponentsBifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
KeywordsHYDROLASE / WRN / Werner / helicase
Function / homology
Function and homology information


positive regulation of hydrolase activity / 3'-flap-structured DNA binding / positive regulation of strand invasion / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / telomere maintenance via semi-conservative replication / DNA geometric change ...positive regulation of hydrolase activity / 3'-flap-structured DNA binding / positive regulation of strand invasion / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / telomere maintenance via semi-conservative replication / DNA geometric change / Y-form DNA binding / telomeric D-loop disassembly / t-circle formation / four-way junction helicase activity / G-quadruplex DNA binding / bubble DNA binding / MutLalpha complex binding / Impaired BRCA2 binding to PALB2 / protein localization to nucleolus / Processive synthesis on the C-strand of the telomere / response to UV-C / Removal of the Flap Intermediate from the C-strand / exonuclease activity / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / DNA metabolic process / DNA synthesis involved in DNA repair / 3'-5' DNA helicase activity / Impaired BRCA2 binding to RAD51 / DNA 3'-5' helicase / replication fork processing / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / mismatch repair / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / 3'-5' exonuclease activity / DNA helicase activity / telomere maintenance / cellular response to starvation / replication fork / determination of adult lifespan / cellular response to gamma radiation / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / base-excision repair / HDR through Homologous Recombination (HRR) / cellular senescence / double-strand break repair / manganese ion binding / chromosome / Processing of DNA double-strand break ends / response to oxidative stress / Regulation of TP53 Activity through Phosphorylation / Hydrolases; Acting on ester bonds / DNA replication / chromosome, telomeric region / nuclear speck / DNA damage response / centrosome / protein-containing complex binding / nucleolus / 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 Å
AuthorsPalte, R.L. / Koglin, M. / Maskos, K. / Tauchert, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: WRN structural flexibility showcased through fragment-based lead discovery of inhibitors.
Authors: Palte, R.L. / Mandal, M. / Sikorska, J. / Villafania, A.B. / Rickard, M.M. / Bauer, R.J. / Buevich, A.V. / Chai, X. / He, J. / Hussain, Z. / Koglin, M. / MacDonald, H.B. / Mansueto, M.S. / ...Authors: Palte, R.L. / Mandal, M. / Sikorska, J. / Villafania, A.B. / Rickard, M.M. / Bauer, R.J. / Buevich, A.V. / Chai, X. / He, J. / Hussain, Z. / Koglin, M. / MacDonald, H.B. / Mansueto, M.S. / Maskos, K. / Methot, J.L. / Robustelli, J. / Soriano, A. / Tauchert, M.J. / Tyagarajan, S. / Zhang, M. / Klein, D.J. / Hicks, J.D. / McLaren, D.G. / Gabelli, S.B. / Wyss, D.F.
History
DepositionDec 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.1Jan 21, 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

Downloads & links

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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)50,7933
Polymers50,4811
Non-polymers3122
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.599, 62.299, 135.107
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: 50480.906 Da / Num. of mol.: 1 / Fragment: UNP residues 500-942
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WRN, RECQ3, RECQL2 / 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-A1BL3 / 6-chloro-7-methyl-1lambda~6~,2,4-benzothiadiazine-1,1,3(2H,4H)-trione


Mass: 246.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7ClN2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 21%-27.5% (w/v) PEG 1500 and 0.1 M MMT pH 5.75-6.25

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→51.47 Å / Num. obs: 21778 / % possible obs: 66.8 % / Redundancy: 3.8 % / CC1/2: 0.995 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 1280 / CC1/2: 0.511

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Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION Jan 31data reduction
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→51.47 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / SU B: 10.743 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26336 504 2.3 %RANDOM
Rwork0.22077 ---
obs0.2218 21252 66.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å2-0 Å2
2---0.57 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2→51.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 16 137 3421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133343
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173197
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.654519
X-RAY DIFFRACTIONr_angle_other_deg1.1971.587356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5645414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44621.488168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52715600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7931524
X-RAY DIFFRACTIONr_chiral_restr0.070.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023750
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02770
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.962.3421653
X-RAY DIFFRACTIONr_mcbond_other0.9612.3421652
X-RAY DIFFRACTIONr_mcangle_it1.6573.5092068
X-RAY DIFFRACTIONr_mcangle_other1.6563.5092069
X-RAY DIFFRACTIONr_scbond_it0.8622.4071690
X-RAY DIFFRACTIONr_scbond_other0.8612.4081691
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.433.5742452
X-RAY DIFFRACTIONr_long_range_B_refined3.46627.2033673
X-RAY DIFFRACTIONr_long_range_B_other3.42527.0883656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å
RfactorNum. reflection% reflection
Rfree0.411 36 -
Rwork0.327 1696 -
obs--73.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2613-1.56570.32083.23930.59512.0773-0.166-0.29930.26280.26810.1878-0.3996-0.19770.1315-0.02180.0583-0.0067-0.0330.0509-0.03970.07199.813-14.836-10.108
22.3616-0.596-0.41342.09570.19361.7029-0.00130.0597-0.1458-0.1362-0.025-0.12820.26240.0550.02640.05450.00610.01010.05670.02590.038410.133-7.375-45.836
37.7708-0.74830.5652.92440.72634.5337-0.1898-0.61320.21130.59680.1146-0.3572-0.03420.12620.07530.15240.0119-0.03470.0578-0.0330.139913.9127.984-34.525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A523 - 727
2X-RAY DIFFRACTION2A735 - 899
3X-RAY DIFFRACTION3A900 - 941

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