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- PDB-9owb: Human WRN helicase in complex with allosteric ligand Compound 6 -

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Basic information

Entry
Database: PDB / ID: 9owb
TitleHuman WRN helicase in complex with allosteric ligand Compound 6
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 / t-circle formation ...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 / t-circle formation / telomeric D-loop disassembly / DNA geometric change / Y-form DNA binding / 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 / Removal of the Flap Intermediate from the C-strand / response to UV-C / 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 3'-5' helicase / DNA metabolic process / 3'-5' DNA helicase activity / DNA synthesis involved in DNA repair / Impaired BRCA2 binding to RAD51 / 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 / telomere maintenance / DNA helicase activity / 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 / chromosome, telomeric region / DNA replication / 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 / HRDC domain / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain ...Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / 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 speciesSpodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsPalte, R.L. / Koglin, M. / Maskos, K. / Tauchert, M.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Slas Discov / Year: 2025
Title: High-throughput evaluation of novel WRN inhibitors.
Authors: Xu, H. / Palte, R.L. / Rickard, M.M. / Kwon, S.W. / Chai, X. / Yuan, J. / Bassett, J. / Moran, J. / Koglin, M. / Musisi, I. / Zhang, M. / Maskos, K. / Tauchert, M.J. / Cheng, Y.S. / Wang, Z. ...Authors: Xu, H. / Palte, R.L. / Rickard, M.M. / Kwon, S.W. / Chai, X. / Yuan, J. / Bassett, J. / Moran, J. / Koglin, M. / Musisi, I. / Zhang, M. / Maskos, K. / Tauchert, M.J. / Cheng, Y.S. / Wang, Z. / Yang, Y. / Banerjee, A. / Chen, J.L. / Bharathan, I. / Rico, L. / Logan, K. / Mansueto, M.S. / Shumway, S. / Methot, J.L. / Bauer, R.J.
History
DepositionJun 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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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
B: Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
C: Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
D: Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,52337
Polymers201,9244
Non-polymers4,59933
Water27,0951504
1
A: Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,68410
Polymers50,4811
Non-polymers1,2039
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6229
Polymers50,4811
Non-polymers1,1418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5608
Polymers50,4811
Non-polymers1,0797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,65710
Polymers50,4811
Non-polymers1,1769
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.085, 58.394, 131.907
Angle α, β, γ (deg.)90.03, 90.00, 90.00
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA511 - 94112 - 442
21ASPASPBB511 - 94112 - 442
12GLUGLUAA510 - 94111 - 442
22GLUGLUCC510 - 94111 - 442
13GLUGLUAA510 - 94111 - 442
23GLUGLUDD510 - 94111 - 442
14ASPASPBB511 - 94112 - 442
24ASPASPCC511 - 94112 - 442
15ASPASPBB511 - 94112 - 442
25ASPASPDD511 - 94112 - 442
16GLUGLUCC510 - 94111 - 442
26GLUGLUDD510 - 94111 - 442

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#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.: 4 / Fragment: UNP residues 500-942
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Gene: WRN, RECQ3, RECQL2 / Production host: Homo sapiens (human)
References: UniProt: Q14191, Hydrolases; Acting on ester bonds, DNA 3'-5' helicase

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Non-polymers , 5 types, 1537 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-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


Mass: 703.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H30ClF3N8O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1504 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20.0% w/v PEG3350, 200 mM ammonium tartrate

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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 EIGER2 X 16M / Detector: PIXEL / Date: Sep 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.556→53.5 Å / Num. obs: 234986 / % possible obs: 94.4 % / Redundancy: 2.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Net I/σ(I): 11.4
Reflection shellResolution: 1.556→1.583 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 8328 / CC1/2: 0.734 / % possible all: 66.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
XDS(VERSION Jan 31data reduction
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→53.46 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 4.176 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19234 8235 3.5 %RANDOM
Rwork0.1497 ---
obs0.15124 226751 94.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.791 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20.01 Å2-0.03 Å2
2--0 Å20.45 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.56→53.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13643 0 297 1504 15444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01314603
X-RAY DIFFRACTIONr_bond_other_d0.0090.01713614
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.6719849
X-RAY DIFFRACTIONr_angle_other_deg1.3041.58731340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44351841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24621.97736
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18915.1032514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.391594
X-RAY DIFFRACTIONr_chiral_restr0.0660.21888
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216787
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023365
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_it2.1983.27190
X-RAY DIFFRACTIONr_mcbond_other2.1963.1997189
X-RAY DIFFRACTIONr_mcangle_it2.8694.8099089
X-RAY DIFFRACTIONr_mcangle_other2.8694.8099090
X-RAY DIFFRACTIONr_scbond_it2.3813.4957413
X-RAY DIFFRACTIONr_scbond_other2.3813.4957414
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9865.11110749
X-RAY DIFFRACTIONr_long_range_B_refined4.02838.37716359
X-RAY DIFFRACTIONr_long_range_B_other3.80637.7816049
X-RAY DIFFRACTIONr_rigid_bond_restr2.443328217
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A55140.02
12B55140.02
21A55380.02
22C55380.02
31A55040.02
32D55040.02
41B55460.01
42C55460.01
51B55120.01
52D55120.01
61C55300.02
62D55300.02
LS refinement shellResolution: 1.56→1.596 Å
RfactorNum. reflection% reflection
Rfree0.313 481 -
Rwork0.288 12409 -
obs--70.32 %

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