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- PDB-5y58: Crystal structure of Ku70/80 and TLC1 -

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Basic information

Entry
Database: PDB / ID: 5y58
TitleCrystal structure of Ku70/80 and TLC1
Components
  • ATP-dependent DNA helicase II subunit 1
  • ATP-dependent DNA helicase II subunit 2
  • TLC1
KeywordsRNA BINDING PROTEIN / telomerase / telomere / protein-RNA complex
Function / homology
Function and homology information


donor selection / mitochondrial double-strand break repair via homologous recombination / subtelomeric heterochromatin formation => GO:0031509 / chromatin organization => GO:0006325 / : / protein localization to chromosome / establishment of protein-containing complex localization to telomere / Ku70:Ku80 complex / cellular response to X-ray / double-strand break repair via break-induced replication ...donor selection / mitochondrial double-strand break repair via homologous recombination / subtelomeric heterochromatin formation => GO:0031509 / chromatin organization => GO:0006325 / : / protein localization to chromosome / establishment of protein-containing complex localization to telomere / Ku70:Ku80 complex / cellular response to X-ray / double-strand break repair via break-induced replication / telomerase RNA binding / recombinational repair / silent mating-type cassette heterochromatin formation / telomeric DNA binding / subtelomeric heterochromatin formation / Neutrophil degranulation / DNA helicase activity / telomere maintenance / double-strand break repair via homologous recombination / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / nuclear envelope / chromatin organization / DNA helicase / damaged DNA binding / chromosome, telomeric region / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Ku70 / 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
RNA / RNA (> 10) / ATP-dependent DNA helicase II subunit 1 / ATP-dependent DNA helicase II subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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
A: ATP-dependent DNA helicase II subunit 1
B: ATP-dependent DNA helicase II subunit 2
X: TLC1
C: ATP-dependent DNA helicase II subunit 1
D: ATP-dependent DNA helicase II subunit 2
Y: TLC1
E: ATP-dependent DNA helicase II subunit 1
F: ATP-dependent DNA helicase II subunit 2
Z: TLC1


Theoretical massNumber of molelcules
Total (without water)445,6259
Polymers445,6259
Non-polymers00
Water5,513306
1
A: ATP-dependent DNA helicase II subunit 1
B: ATP-dependent DNA helicase II subunit 2
X: TLC1


Theoretical massNumber of molelcules
Total (without water)148,5423
Polymers148,5423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25560 Å2
ΔGint-160 kcal/mol
Surface area56270 Å2
MethodPISA
2
C: ATP-dependent DNA helicase II subunit 1
D: ATP-dependent DNA helicase II subunit 2
Y: TLC1


Theoretical massNumber of molelcules
Total (without water)148,5423
Polymers148,5423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25560 Å2
ΔGint-160 kcal/mol
Surface area55790 Å2
MethodPISA
3
E: ATP-dependent DNA helicase II subunit 1
F: ATP-dependent DNA helicase II subunit 2
Z: TLC1


Theoretical massNumber of molelcules
Total (without water)148,5423
Polymers148,5423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25560 Å2
ΔGint-160 kcal/mol
Surface area55930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.296, 115.159, 115.847
Angle α, β, γ (deg.)77.430, 78.480, 63.730
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ATP-dependent DNA helicase II subunit 1 / ATP-dependent DNA helicase II subunit Ku70 / High affinity DNA-binding factor subunit 1


Mass: 67709.078 Da / Num. of mol.: 3 / Fragment: UNP residues 28-602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YKU70, HDF1, NES24, YMR284W, YM8021.10 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High Five / References: UniProt: P32807, DNA helicase
#2: 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: 71193.648 Da / Num. of mol.: 3
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 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High Five / References: UniProt: Q04437, DNA helicase
#3: RNA chain TLC1


Mass: 9638.777 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: in vitro transcription
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGlmS / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 3.03 Å3/Da / Density % sol: 59.35 % / Mosaicity: 0.487 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 8
Details: 0.2 M calcium acetate, 0.1 M imidazole, 10% PEG8000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL18U110.97853
SYNCHROTRONSSRF BL19U120.97853
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELMay 23, 2016
DECTRIS PILATUS 6M2PIXELMay 23, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978531
21
ReflectionResolution: 2.8→50 Å / Num. obs: 121941 / % possible obs: 93.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 43.34 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.045 / Rrim(I) all: 0.089 / Χ2: 0.881 / Net I/σ(I): 6.6 / Num. measured all: 463727
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.93.80.556125300.8030.3260.6450.88896
2.9-3.023.80.405123800.8720.2380.470.90295.7
3.02-3.153.90.269123820.9320.1570.3110.91495.2
3.15-3.323.80.194122810.9540.1130.2240.94594.7
3.32-3.533.80.136122440.9760.080.1580.97494.1
3.53-3.83.80.101120320.9810.060.1170.96192.8
3.8-4.183.70.072117970.9880.0430.0840.91990.9
4.18-4.793.60.059106240.9880.0360.0690.93781.8
4.79-6.033.90.051128080.9920.030.0590.75998.4
6.03-503.90.039128630.9960.0230.0460.65199.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
PDB_EXTRACT3.22data extraction
XDSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→44.107 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 5877 4.97 %RANDOM
Rwork0.2153 112260 --
obs0.2175 118137 91.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.24 Å2 / Biso mean: 68.7218 Å2 / Biso min: 10.79 Å2
Refinement stepCycle: final / Resolution: 2.8→44.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27091 1923 0 306 29320
Biso mean---40.89 -
Num. residues----3427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00329841
X-RAY DIFFRACTIONf_angle_d0.58740713
X-RAY DIFFRACTIONf_chiral_restr0.0244647
X-RAY DIFFRACTIONf_plane_restr0.0024869
X-RAY DIFFRACTIONf_dihedral_angle_d12.4211673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-2.83190.35151410.29082887302869
2.8319-2.86520.36531430.27893175331879
2.8652-2.90010.34341690.27023637380688
2.9001-2.93680.31351770.27313729390692
2.9368-2.97540.3132110.27563859407094
2.9754-3.01620.36971910.29123823401495
3.0162-3.05930.35181990.27353885408494
3.0593-3.10490.35932220.25363797401995
3.1049-3.15340.27522140.24323904411896
3.1534-3.20510.33162160.24143851406794
3.2051-3.26040.28952010.24033853405495
3.2604-3.31960.30271950.23843860405594
3.3196-3.38350.31311860.23073833401994
3.3835-3.45250.26462080.23023823403194
3.4525-3.52750.2691910.23333843403494
3.5275-3.60960.28611870.22533846403393
3.6096-3.69980.22411630.21373761392493
3.6998-3.79980.26251930.21073746393992
3.7998-3.91150.2382130.20753699391291
3.9115-4.03770.2391980.20453684388290
4.0377-4.18190.23521810.19623729391091
4.1819-4.34920.24582050.1943571377688
4.3492-4.54690.21081800.1913308348882
4.5469-4.78640.21741610.18153052321375
4.7864-5.08590.21021960.1734026422298
5.0859-5.47790.21352290.18434026425599
5.4779-6.02790.26332330.20634002423599
6.0279-6.89730.2592240.21434027425199
6.8973-8.6790.22892370.19834021425899
8.679-44.11240.19242130.18654003421698
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)
11.8314-0.6886-0.30431.16210.61841.3945-0.2563-0.53650.12620.26780.2031-0.26830.02390.09140.04650.17710.0847-0.10210.32230.0070.25240.34190.0994134.8163
21.89120.0858-0.16591.96240.20031.0145-0.190.3796-0.4235-0.61160.1451-0.52740.34880.15230.02460.3250.04590.17930.2721-0.09390.43289.540471.9823105.1682
32.7175-0.1475-1.27564.06140.97531.924-0.2983-0.0691-0.0173-0.02530.11960.38250.0065-0.27020.21010.48740.002-0.00770.2631-0.08260.3986-6.732572.3535106.0173
41.42280.23760.1631.47360.71481.225-0.05620.01420.1141-0.0039-0.12680.2947-0.1069-0.1680.09490.1592-0.0005-0.00240.13360.00380.261-59.29118.5053121.3165
51.2713-0.12360.23681.47130.08551.5609-0.0795-0.28030.40860.33010.0317-0.3937-0.4270.457-0.07230.3891-0.1159-0.11740.3234-0.14380.4732-29.8718132.9884136.0446
61.15261.61161.16994.59290.272.1357-0.0547-0.1584-0.0617-0.215-0.0471-0.04290.2724-0.04170.11350.39980.0912-0.0820.5189-0.06340.2656-27.2232117.0481134.1851
71.356-0.70610.2791.0368-0.16331.37090.15220.8884-0.8769-0.0917-0.0530.06570.43470.1837-0.09020.298-0.1129-0.1460.4498-0.60980.6939-37.926365.844585.3757
82.0244-0.1185-0.00471.07960.09132.10930.22471.04170.1582-0.1347-0.0350.5556-0.3903-0.53720.04950.28310.0568-0.12510.8101-0.11550.3452-60.146892.637576.3165
94.6758-0.70260.39911.2636-2.13233.75810.25350.0953-0.45960.1619-0.10840.1009-0.13810.2302-0.13750.2605-0.08490.0470.4863-0.18490.4518-56.646394.145692.1351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA28 - 584
2X-RAY DIFFRACTION2chain BB2 - 621
3X-RAY DIFFRACTION3chain XX286 - 315
4X-RAY DIFFRACTION4chain CC28 - 584
5X-RAY DIFFRACTION5chain DD2 - 621
6X-RAY DIFFRACTION6chain YY286 - 315
7X-RAY DIFFRACTION7chain EE28 - 584
8X-RAY DIFFRACTION8chain FF2 - 621
9X-RAY DIFFRACTION9chain ZZ286 - 315

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