[English] 日本語
Yorodumi
- PDB-5y59: Crystal structure of Ku80 and Sir4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5y59
TitleCrystal structure of Ku80 and Sir4
Components
  • ATP-dependent DNA helicase II subunit 2
  • Sir4p
KeywordsPROTEIN BINDING / telomerase / telomere / protein-protein complex
Function / homology
Function and homology information


donor selection / protein localization to chromosome / establishment of protein-containing complex localization to telomere / Ku70:Ku80 complex / cellular response to X-ray / telomerase RNA binding / recombinational repair / telomeric DNA binding / subtelomeric heterochromatin formation / DNA helicase activity ...donor selection / protein localization to chromosome / establishment of protein-containing complex localization to telomere / Ku70:Ku80 complex / cellular response to X-ray / telomerase RNA binding / recombinational repair / telomeric DNA binding / subtelomeric heterochromatin formation / DNA helicase activity / Neutrophil degranulation / telomere maintenance / double-strand break repair via homologous recombination / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / chromatin organization / DNA helicase / chromosome, telomeric region / damaged DNA binding / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 C-terminal arm / Ku70/Ku80 N-terminal alpha/beta domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
: / ATP-dependent DNA helicase II subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.402 Å
AuthorsChen, H. / Xue, J. / Wu, J. / Lei, M.
CitationJournal: Cell / Year: 2018
Title: Structural Insights into Yeast Telomerase Recruitment to Telomeres
Authors: Chen, H. / Xue, J. / Churikov, D. / Hass, E.P. / Shi, S. / Lemon, L.D. / Luciano, P. / Bertuch, A.A. / Zappulla, D.C. / Geli, V. / Wu, J. / Lei, M.
History
DepositionAug 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: ATP-dependent DNA helicase II subunit 2
C: Sir4p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2193
Polymers24,1232
Non-polymers961
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-23 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.472, 79.472, 82.926
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein ATP-dependent DNA helicase II subunit 2 / ATP-dependent DNA helicase II subunit Ku80 / High affinity DNA-binding factor subunit 2 / Yeast Ku80


Mass: 22759.916 Da / Num. of mol.: 1 / Fragment: vWA domain, UNP residues 2-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YKU80, HDF2, YMR106C, YM9718.05C / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q04437, DNA helicase
#2: Protein/peptide Sir4p


Mass: 1362.640 Da / Num. of mol.: 1 / Fragment: Ku binding motif, UNP residues 104-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: Zymaflore VL3 / Gene: VL3_0944 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E7QD18
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.75 % / Mosaicity: 0.242 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 7.5 / Details: 0.1 M HEPES, 2.0 M ammonium sulfate

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL18U110.97851
SYNCHROTRONSSRF BL19U120.97851
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELOct 17, 2016
DECTRIS PILATUS 6M2PIXELOct 17, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978511
21
ReflectionResolution: 2.4→50 Å / Num. obs: 12169 / % possible obs: 99.6 % / Redundancy: 18 % / Biso Wilson estimate: 34.82 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.017 / Rrim(I) all: 0.073 / Χ2: 0.967 / Net I/σ(I): 6.2 / Num. measured all: 219073
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4911.40.88811560.8330.2530.9270.99796.2
2.49-2.5914.10.75911830.9440.2020.7870.99999.9
2.59-2.718.70.72312060.9660.170.7431.014100
2.7-2.8520.30.53112070.9830.120.5451.021100
2.85-3.0219.70.32911960.9920.0760.3381.021100
3.02-3.2618.90.17512110.9970.0410.1791.032100
3.26-3.5820.20.10212330.9990.0230.1051.03100
3.58-4.119.30.06212120.9990.0140.0640.997100
4.1-5.1719.70.03912520.9990.0090.040.86100
5.17-5017.30.031131310.0070.0320.714100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.402→27.642 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 592 5.4 %
Rwork0.2012 10365 -
obs0.2037 10957 89.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.38 Å2 / Biso mean: 59.0118 Å2 / Biso min: 16.17 Å2
Refinement stepCycle: final / Resolution: 2.402→27.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 5 35 1632
Biso mean--98.57 52.16 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011614
X-RAY DIFFRACTIONf_angle_d1.3062178
X-RAY DIFFRACTIONf_chiral_restr0.064265
X-RAY DIFFRACTIONf_plane_restr0.004270
X-RAY DIFFRACTIONf_dihedral_angle_d14.323610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4021-2.64360.31981080.23991688179660
2.6436-3.02580.28121610.228828382999100
3.0258-3.81060.24731520.208228893041100
3.8106-27.64380.22341710.18062950312199
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)
14.76650.2482-1.06133.2004-0.79797.086-0.06640.7438-0.3052-0.28630.0240.05691.04470.0024-0.00720.29560.0534-0.00420.2879-0.12540.270725.029719.5094-10.3744
26.7633-1.1101-0.13814.38910.02544.7056-0.25830.4879-0.71570.13210.3552-0.65711.57090.80410.92291.12720.23340.32621.1962-0.53970.826237.835212.3659-24.2123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain BB2 - 199
2X-RAY DIFFRACTION2chain CC104 - 115

+
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://pdbjlvh1.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