1JEY

Crystal Structure of the Ku heterodimer bound to DNA

> Summary

Summary for 1JEY

Related1JEQ
DescriptorKu Heterodimer/DNA complex
Functional Keywordsdouble-strand dna break repair, non-homologous end-joining, protein-nucleic acid complex, alpha/beta domain, beta barrel, helical c-terminal arm, sap domain, dna binding protein-dna complex, dna binding protein/dna
Biological sourceHomo sapiens (human)
Cellular locationNucleus P12956 P13010
Total number of polymer chains4
Total molecular weight150968.95
Authors
Walker, J.R.,Corpina, R.A.,Goldberg, J. (deposition date: 2001-06-19, release date: 2001-08-10, modification date: 2009-02-24)
Primary citation
Walker, J.R.,Corpina, R.A.,Goldberg, J.
Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair.
Nature, 412:607-614, 2001
PubMed: 11493912
DOI: 10.1038/35088000
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.5 Å)
NMR Information
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Structure validation

ClashscoreRamachandran outliersSidechain outliers150.6%2.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1jey
no rotation
Molmil generated image of 1jey
rotated about x axis by 90°
Molmil generated image of 1jey
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
CDNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')polymer216506.21
DDNA (34-MER)polymer3410325.81
AKu70polymer60969945.71
UniProt (P12956)
Pfam (PF02037)
Pfam (PF02735)
Pfam (PF03730)
Pfam (PF03731)
Homo sapiens (human)@PDBjHOMO SAPIENS THYROID AUTOANTIGEN 70KD
BKu80polymer56564191.21
UniProt (P13010)
Pfam (PF02735)
Pfam (PF03730)
Pfam (PF03731)
Homo sapiens (human)@PDBjDNA REPAIR PROTEIN XRCC5
waterwater18.0255

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight150968.9
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight150968.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Cell axes83.920126.305126.436
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits24.74 - 2.50
the highest resolution shell value2.660 - 2.500
R-factor0.22 (0.218*)
R-work0.21800
the highest resolution shell value0.261
R-free0.28000 (0.27600*)
the highest resolution shell value0.345
RMSD bond length0.007 (0.005*)
RMSD bond angle1.300 (1.220*)

Data Collection Statistics

Resolution limits25.00 - 2.50
the highest resolution shell value -
Number of reflections46176 (46385*)
Number of measurements141891*
Rmerge_l_obs0.065
the highest resolution shell value0.306 (0.311*)
Completeness96.4
the highest resolution shell value82.3*
Redundancy3.1
the highest resolution shell value2.7
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP8320 (22*)*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
111PEG 350 monomethyl ether
211Tris-HCl
311MgCl2
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropprotein18 (mg/ml)
21reservoirPEG350MME26 (%)
31reservoirTris-HCl50 (mM)pH8.0
41reservoir5 (mM)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
B0005829cellular_componentcytosol
B0043564cellular_componentKu70:Ku80 complex
B0016020cellular_componentmembrane
B0070419cellular_componentnonhomologous end joining complex
B0000784cellular_componentnuclear chromosome, telomeric region
B0000783cellular_componentnuclear telomere cap complex
B0005730cellular_componentnucleolus
B0005654cellular_componentnucleoplasm
B0005634cellular_componentnucleus
B0005886cellular_componentplasma membrane
B0005524molecular_functionATP binding
B0004003molecular_functionATP-dependent DNA helicase activity
B0003684molecular_functiondamaged DNA binding
B0003677molecular_functionDNA binding
B0003690molecular_functiondouble-stranded DNA binding
B0044877molecular_functionmacromolecular complex binding
B0044822molecular_functionpoly(A) RNA binding
B0008022molecular_functionprotein C-terminus binding
B0042162molecular_functiontelomeric DNA binding
B0044212molecular_functiontranscription regulatory region DNA binding
B0031625molecular_functionubiquitin protein ligase binding
B0008283biological_processcell proliferation
B0071480biological_processcellular response to gamma radiation
B0071481biological_processcellular response to X-ray
B0032508biological_processDNA duplex unwinding
B0006310biological_processDNA recombination
B0006281biological_processDNA repair
B0006302biological_processdouble-strand break repair
B0006303biological_processdouble-strand break repair via nonhomologous end joining
B0075713biological_processestablishment of integrated proviral latency
B0060218biological_processhematopoietic stem cell differentiation
B0045087biological_processinnate immune response
B1904430biological_processnegative regulation of t-circle formation
B0045892biological_processnegative regulation of transcription, DNA-templated
B0050769biological_processpositive regulation of neurogenesis
B0032481biological_processpositive regulation of type I interferon production
B0048660biological_processregulation of smooth muscle cell proliferation
B0000723biological_processtelomere maintenance
B0006351biological_processtranscription, DNA-templated
B0016032biological_processviral process
A0005829cellular_componentcytosol
A0043564cellular_componentKu70:Ku80 complex
A0016020cellular_componentmembrane
A0070419cellular_componentnonhomologous end joining complex
A0000784cellular_componentnuclear chromosome, telomeric region
A0000783cellular_componentnuclear telomere cap complex
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0005667cellular_componenttranscription factor complex
A0051575molecular_function5'-deoxyribose-5-phosphate lyase activity
A0005524molecular_functionATP binding
A0004003molecular_functionATP-dependent DNA helicase activity
A0003684molecular_functiondamaged DNA binding
A0003677molecular_functionDNA binding
A0003690molecular_functiondouble-stranded DNA binding
A0044877molecular_functionmacromolecular complex binding
A0044822molecular_functionpoly(A) RNA binding
A0008022molecular_functionprotein C-terminus binding
A0042162molecular_functiontelomeric DNA binding
A0044212molecular_functiontranscription regulatory region DNA binding
A0071480biological_processcellular response to gamma radiation
A0071481biological_processcellular response to X-ray
A0032508biological_processDNA duplex unwinding
A0006266biological_processDNA ligation
A0006310biological_processDNA recombination
A0006281biological_processDNA repair
A0006302biological_processdouble-strand break repair
A0097680biological_processdouble-strand break repair via classical nonhomologous end joining
A0006303biological_processdouble-strand break repair via nonhomologous end joining
A0075713biological_processestablishment of integrated proviral latency
A0045087biological_processinnate immune response
A0045892biological_processnegative regulation of transcription, DNA-templated
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0045893biological_processpositive regulation of transcription, DNA-templated
A0032481biological_processpositive regulation of type I interferon production
A0051290biological_processprotein heterotetramerization
A0048660biological_processregulation of smooth muscle cell proliferation
A0000723biological_processtelomere maintenance
A0006351biological_processtranscription, DNA-templated
A0016032biological_processviral process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Schiff-base intermediate with DNA; for 5'-deoxyribose-5-phosphate lyase activity (Probable).
ChainResidueDetails
ANA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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