[English] 日本語
Yorodumi
- PDB-8yle: Crystal structure of Werner syndrome helicase complexed with AMP-PCP -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / t-circle formation / telomeric D-loop disassembly ...3'-flap-structured DNA binding / positive regulation of strand invasion / telomeric G-quadruplex DNA binding / 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 / t-circle formation / telomeric D-loop disassembly / DNA geometric change / Y-form DNA binding / G-quadruplex DNA binding / bubble DNA binding / MutLalpha complex binding / Impaired BRCA2 binding to PALB2 / Processive synthesis on the C-strand of the telomere / protein localization to nucleolus / Removal of the Flap Intermediate from the C-strand / response to UV-C / 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) / exonuclease activity / 3'-5' DNA helicase activity / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA 3'-5' helicase / HDR through Single Strand Annealing (SSA) / DNA metabolic process / Impaired BRCA2 binding to RAD51 / DNA synthesis involved in DNA repair / replication fork processing / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / SUMOylation of DNA damage response and repair proteins / DNA helicase activity / four-way junction DNA binding / 3'-5' exonuclease activity / telomere maintenance / cellular response to starvation / replication fork / determination of adult lifespan / isomerase activity / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / cellular response to gamma radiation / 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 / Regulation of TP53 Activity through Phosphorylation / response to oxidative stress / Hydrolases; Acting on ester bonds / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromosome, telomeric region / DNA replication / 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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more