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- PDB-5y59: Crystal structure of Ku80 and Sir4 -

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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 / telomerase RNA binding / recombinational repair / telomeric DNA binding / subtelomeric heterochromatin formation / Neutrophil degranulation / telomere maintenance ...donor selection / protein localization to chromosome / establishment of protein-containing complex localization to telomere / Ku70:Ku80 complex / telomerase RNA binding / recombinational repair / telomeric DNA binding / subtelomeric heterochromatin formation / Neutrophil degranulation / telomere maintenance / helicase activity / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / chromatin organization / DNA helicase / damaged DNA binding / chromosome, telomeric region / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Ku80 / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 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

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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

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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

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