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- PDB-8yle: Crystal structure of Werner syndrome helicase complexed with AMP-PCP -

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Basic information

Entry
Database: PDB / ID: 8yle
TitleCrystal structure of Werner syndrome helicase complexed with AMP-PCP
ComponentsBifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
KeywordsHYDROLASE / DNA repair helicase
Function / homology
Function and homology information


3'-flap-structured DNA binding / positive regulation of strand invasion / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / positive regulation of hydrolase activity / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / telomere maintenance via semi-conservative replication / G-quadruplex DNA unwinding ...3'-flap-structured DNA binding / positive regulation of strand invasion / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / positive regulation of hydrolase activity / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / telomere maintenance via semi-conservative replication / G-quadruplex DNA unwinding / t-circle formation / telomeric D-loop disassembly / Y-form DNA binding / DNA 3'-5' helicase / four-way junction helicase activity / G-quadruplex DNA binding / MutLalpha complex binding / bubble DNA binding / Processive synthesis on the C-strand of the telomere / Impaired BRCA2 binding to PALB2 / Removal of the Flap Intermediate from the C-strand / protein localization to nucleolus / 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 / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / response to UV-C / Resolution of D-loop Structures through Holliday Junction Intermediates / exonuclease activity / DNA duplex unwinding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA metabolic process / 3'-5' DNA helicase activity / DNA synthesis involved in DNA repair / replication fork processing / DNA unwinding involved in DNA replication / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / isomerase activity / 3'-5' exonuclease activity / cellular response to starvation / DNA helicase activity / telomere maintenance / replication fork / determination of adult lifespan / double-strand break repair via homologous recombination / base-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / cellular response to gamma radiation / cellular senescence / double-strand break repair / chromosome / manganese ion binding / Processing of DNA double-strand break ends / response to oxidative stress / Regulation of TP53 Activity through Phosphorylation / DNA replication / chromosome, telomeric region / Hydrolases; Acting on ester bonds / nuclear speck / centrosome / DNA damage response / chromatin binding / 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 / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain ...Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / HRDC-like superfamily / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / Winged helix DNA-binding domain superfamily / Ribonuclease H-like superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsYang, Y. / Fu, L. / Sun, X. / Cheng, H. / Chen, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of werner syndrome helicase complexed with AMP-PCP at 1.86 Angstroms resolution.
Authors: Chen, R.
History
DepositionMar 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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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)49,7646
Polymers49,0031
Non-polymers7605
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.663, 89.561, 54.359
Angle α, β, γ (deg.)90.000, 102.880, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 49003.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WRN, RECQ3, RECQL2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q14191, Hydrolases; Acting on ester bonds, DNA helicase
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: pH 6.5,0.1 M Amino acids,0.1 M Buffer System 1, 30.00% % v/v EDO_P8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.86→30.05 Å / Num. obs: 38310 / % possible obs: 98.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 22.22 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.07505 / Rrim(I) all: 0.1585 / Net I/σ(I): 8.28
Reflection shellResolution: 1.86→1.926 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.123 / Mean I/σ(I) obs: 2.23 / Num. unique obs: 3782 / CC1/2: 0.631 / CC star: 0.88 / % possible all: 97.54

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→30.05 Å / SU ML: 0.2025 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8709
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2143 1948 5.09 %
Rwork0.1833 36325 -
obs0.1849 38273 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.67 Å2
Refinement stepCycle: LAST / Resolution: 1.86→30.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 41 235 3590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583426
X-RAY DIFFRACTIONf_angle_d0.79664627
X-RAY DIFFRACTIONf_chiral_restr0.0505513
X-RAY DIFFRACTIONf_plane_restr0.0065586
X-RAY DIFFRACTIONf_dihedral_angle_d13.69941291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.910.29851510.2812551X-RAY DIFFRACTION97.44
1.91-1.960.26791160.24762553X-RAY DIFFRACTION97.59
1.96-2.020.26461440.2162586X-RAY DIFFRACTION97.71
2.02-2.080.24771320.19912594X-RAY DIFFRACTION98.63
2.08-2.160.25011210.1942607X-RAY DIFFRACTION98.34
2.16-2.240.21421330.19372606X-RAY DIFFRACTION98.56
2.24-2.340.24271570.19812561X-RAY DIFFRACTION98.59
2.34-2.470.21461410.18432599X-RAY DIFFRACTION98.35
2.47-2.620.21411380.182618X-RAY DIFFRACTION98.64
2.62-2.820.21551670.18412547X-RAY DIFFRACTION98.33
2.82-3.110.24231420.18232607X-RAY DIFFRACTION98.53
3.11-3.560.18611220.16772620X-RAY DIFFRACTION98.53
3.56-4.480.1761400.15562609X-RAY DIFFRACTION98.35
4.48-30.050.19641440.17782667X-RAY DIFFRACTION99.05
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)
10.2524942321250.222106687630.11762079350.4716082841010.02579807640260.218856492650.0202573581925-0.006860447947710.002122773887810.00954706700249-0.022744436810.002183063727220.04528570083850.0277184737616-1.32148372212E-60.1646485592750.003367174787460.007547744581160.1329145605060.0164340326120.128778303814-2.45112346256-11.851578489426.0942217589
20.2946004846910.1890188322490.1253279590110.600980337694-0.05005176667230.1771931853350.0157001816805-0.01114789653450.0486316772518-0.05666708731160.000819551972756-0.13345857257-0.1286768034330.1331026374397.96048017532E-60.162892896655-0.00762797702185-0.006264935195830.176076802782-0.00111847186710.14885633710512.8725318757-2.2619399869324.5017316236
30.2224199206070.1422862258810.09429878399790.2828391318770.0905160225590.002047774386350.0607840684170.00641991830017-0.0583221165416-0.128029281380.009395023790370.0493198184130.11925532844-0.01947291359950.008418403360240.1262718591210.008713881390740.01495389267150.121541907762-0.0002845502101460.0956996429917-3.18973052822-4.256393012237.30473501168
4-0.0843080068438-0.04215949566770.1974039652870.2889277574220.09692674663590.304415487505-0.01265788301990.02060674211360.02298098695250.0597123471210.0114311307499-0.00319994142908-0.0613882536431-0.0201612714986-2.90051830047E-60.11879098772-0.004123884871480.007250935016990.1212174219960.01465028739040.13471330081-7.4511489379113.91014711249.54834766407
50.1539694592020.0298477261040.2262541295780.3646672029920.2403072984140.261020865649-0.01027145058570.1652124004-0.08090521357140.0716648301126-0.0380105548324-0.2700387658780.07452158041970.1547218527730.02672239304120.06206557081050.01101854610590.03821603108460.2031393332050.0481047068660.21047231492-3.116798685135.79761782328-2.5029059212
60.0759402399735-0.0673086200111-0.1295698336810.593079594073-0.4191670383240.80729559273-0.0720440033260.0726351982773-0.168044961052-0.1164118007920.221146311427-0.1354615354140.284330482720.121774667340.1895536216820.1452935285690.01418256802660.02347107433750.18478308725-0.08577647423170.1868926893-3.07409767092-4.51466739277-5.29063220266
70.427917684885-0.111147771156-0.002429329412430.256902739452-0.200589842330.4729877641260.05145318714020.286009628622-0.18371128041-0.274069472184-0.02607280423340.01524828260320.359611629375-0.240553880111-0.0209832845960.171125346272-0.0343974875284-0.02265892364440.206717936758-0.01311450241330.219384501227-19.8288539982-7.60577362364-2.31128187062
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 81 )9 - 811 - 73
22chain 'A' and (resid 82 through 176 )82 - 17674 - 164
33chain 'A' and (resid 177 through 239 )177 - 239165 - 227
44chain 'A' and (resid 240 through 337 )240 - 337228 - 325
55chain 'A' and (resid 338 through 368 )338 - 368326 - 356
66chain 'A' and (resid 369 through 401 )369 - 401357 - 389
77chain 'A' and (resid 402 through 428 )402 - 428390 - 416

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