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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KU HETERODIMER BOUND TO DNA
 
Authors :  J. R. Walker, R. A. Corpina, J. Goldberg
Date :  19 Jun 01  (Deposition) - 10 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Double-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 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Walker, R. A. Corpina, J. Goldberg
Structure Of The Ku Heterodimer Bound To Dna And Its Implications For Double-Strand Break Repair.
Nature V. 412 607 2001
PubMed-ID: 11493912  |  Reference-DOI: 10.1038/35088000
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP *CP*G)-3')
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (34-MER)
    ChainsD
    EngineeredYES
    SyntheticYES
 
Molecule 3 - KU70
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFASTBAC HT
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GeneG22P1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHOMO SAPIENS THYROID AUTOANTIGEN 70KD
 
Molecule 4 - KU80
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFASTBAC HT
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentRESIDUES 1-565
    GeneXRCC5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDNA REPAIR PROTEIN XRCC5

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1JEY)

(-) Sites  (0, 0)

(no "Site" information available for 1JEY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JEY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JEY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014724L463FXRCC5_HUMANPolymorphism1805380BL463F
2UniProtVAR_053784I508VXRCC5_HUMANPolymorphism2287558BI508V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JEY)

(-) Exons   (24, 24)

Asymmetric/Biological Unit (24, 24)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003600791aENSE00001816656chr22:42017123-42017349227XRCC6_HUMAN-00--
1.2eENST000003600792eENSE00002150395chr22:42017994-4201809097XRCC6_HUMAN1-28280--
1.3aENST000003600793aENSE00000656031chr22:42024122-42024234113XRCC6_HUMAN28-65381A:34-6532
1.4aENST000003600794aENSE00000656042chr22:42032117-42032255139XRCC6_HUMAN66-112471A:66-11247
1.5ENST000003600795ENSE00000656049chr22:42032520-42032774255XRCC6_HUMAN112-197861A:112-19786
1.6ENST000003600796ENSE00000656053chr22:42033612-42033795184XRCC6_HUMAN197-258621A:197-258 (gaps)62
1.7ENST000003600797ENSE00000656057chr22:42042900-42043086187XRCC6_HUMAN258-320631A:258-32063
1.8ENST000003600798ENSE00000880476chr22:42046727-42046895169XRCC6_HUMAN321-377571A:321-37757
1.9ENST000003600799ENSE00000880477chr22:42049533-42049694162XRCC6_HUMAN377-431551A:377-43155
1.10aENST0000036007910aENSE00000656076chr22:42052907-42053036130XRCC6_HUMAN431-474441A:431-47444
1.11ENST0000036007911ENSE00000656085chr22:42054256-42054356101XRCC6_HUMAN474-508351A:474-50835
1.12aENST0000036007912aENSE00000656094chr22:42057335-42057448114XRCC6_HUMAN508-546391A:508-53427
1.13cENST0000036007913cENSE00001525046chr22:42059626-42060043418XRCC6_HUMAN546-609640--

2.1ENST000003921331ENSE00001606905chr2:216972187-21697225569XRCC5_HUMAN-00--
2.2ENST000003921332ENSE00001685529chr2:216972376-21697242146XRCC5_HUMAN-00--
2.3aENST000003921333aENSE00001722417chr2:216973814-216974180367XRCC5_HUMAN1-771B:6-72
2.5aENST000003921335aENSE00001702382chr2:216977739-216977852114XRCC5_HUMAN8-45381B:8-4538
2.6bENST000003921336bENSE00001074754chr2:216981382-216981565184XRCC5_HUMAN46-107621B:46-10762
2.6gENST000003921336gENSE00001741685chr2:216982469-21698251749XRCC5_HUMAN107-123171B:107-12317
2.7cENST000003921337cENSE00001791529chr2:216983766-216983888123XRCC5_HUMAN123-164421B:123-16442
2.8ENST000003921338ENSE00001074723chr2:216986785-216986976192XRCC5_HUMAN164-228651B:164-228 (gaps)65
2.9aENST000003921339aENSE00000785536chr2:216990640-216990754115XRCC5_HUMAN228-266391B:228-26639
2.10aENST0000039213310aENSE00000785538chr2:216992259-216992397139XRCC5_HUMAN267-313471B:267-31347
2.12ENST0000039213312ENSE00000785539chr2:216995598-216995710113XRCC5_HUMAN313-350381B:313-35038
2.13ENST0000039213313ENSE00000785540chr2:216997048-21699711063XRCC5_HUMAN351-371211B:351-37121
2.14ENST0000039213314ENSE00000417070chr2:217001811-217001948138XRCC5_HUMAN372-417461B:372-41746
2.15ENST0000039213315ENSE00000785542chr2:217002812-21700290291XRCC5_HUMAN418-448311B:418-44831
2.16ENST0000039213316ENSE00000785543chr2:217005909-217006042134XRCC5_HUMAN448-492451B:448-49245
2.17ENST0000039213317ENSE00001316333chr2:217012806-217012999194XRCC5_HUMAN493-557651B:493-54553
2.18ENST0000039213318ENSE00000785545chr2:217024791-21702488494XRCC5_HUMAN557-588320--
2.19ENST0000039213319ENSE00001312814chr2:217026702-21702677170XRCC5_HUMAN589-612240--
2.20ENST0000039213320ENSE00001299331chr2:217054948-217055057110XRCC5_HUMAN612-648370--
2.21ENST0000039213321ENSE00001319280chr2:217057362-21705745897XRCC5_HUMAN649-681330--
2.22ENST0000039213322ENSE00001306763chr2:217059642-21705970968XRCC5_HUMAN681-703230--
2.23bENST0000039213323bENSE00001290848chr2:217069045-21706911975XRCC5_HUMAN704-728250--
2.24eENST0000039213324eENSE00001702636chr2:217069911-2170710261116XRCC5_HUMAN729-73240--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:493
 aligned with XRCC6_HUMAN | P12956 from UniProtKB/Swiss-Prot  Length:609

    Alignment length:501
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533 
          XRCC6_HUMAN    34 GRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDY 534
               SCOP domains d1jeya2 A:34-253 Ku70 subunit N-terminal domain                                                                                                                                                                             d1jeya1 A:254-534 Ku70 subunit middle domain                                                                                                                                                                                                                                              SCOP domains
               CATH domains -1jeyA01 A:35-250  [code=3.40.50.410, no name defined]                                                                                                                                                                   1jeyA02 A:251-278,A:342-439 1jeyA03 A:279-341 Ku70, bridge and pillars                     1jeyA02 A:251-278,A:342-439  [code=2.40.290.10, no name defined]                                  1jeyA04 A:440-533  [code=1.10.1600.10, no name defined]                                       - CATH domains
               Pfam domains ---Ku_N-1jeyA03 A:37-256                                                                                                                                                                                                       ----Ku-1jeyA01 A:261-463                                                                                                                                                                                       -----Ku_C-1jeyA02 A:469-534                                             Pfam domains
         Sec.struct. author .eeeeeeeee.hhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee.............eeeeeeee..hhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....eeeeeeeeee........hhhhhhhhhhhhhhhhhhheeeeeee...........hhhhh..--------.......hhhhhhhhhhhhhh.....eeeeee.....eeeeeee...........eeee......eeeeeeeee.......hhh.eeeeeee..eeeeehhhhhhhh......eeeeeeeee.hhhhhhhh....eeeee....eehhhhhhhhhhhhhhhh.eeeeeeee.......eeeeeeee..ee.....eee..eeeeee..hhhh............hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:34-65         Exon 1.4a  PDB: A:66-112 UniProt: 66-112       ------------------------------------------------------------------------------------Exon 1.6  PDB: A:197-258 (gaps) UniProt: 197-258              --------------------------------------------------------------Exon 1.8  PDB: A:321-377 UniProt: 321-377                -----------------------------------------------------Exon 1.10a  PDB: A:431-474 UniProt: 431-474 ---------------------------------Exon 1.12a  PDB: A:508-534  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------Exon 1.5  PDB: A:112-197 UniProt: 112-197                                             ------------------------------------------------------------Exon 1.7  PDB: A:258-320 UniProt: 258-320                      --------------------------------------------------------Exon 1.9  PDB: A:377-431 UniProt: 377-431              ------------------------------------------Exon 1.11  PDB: A:474-508          -------------------------- Transcript 1 (2)
                 1jey A  34 GRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIIS--------VHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDY 534
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213        |-       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533 
                                                                                                                                                                                                                      222      231                                                                                                                                                                                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:530
 aligned with XRCC5_HUMAN | P13010 from UniProtKB/Swiss-Prot  Length:732

    Alignment length:540
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545
          XRCC5_HUMAN     6 NKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAKKK 545
               SCOP domains d1jeyb2 B:6-241 Ku80 subunit N-terminal domain                                                                                                                                                                                              d1jeyb1 B:242-545 Ku80 subunit middle domain                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1jeyB01 B:6-242  [code=3.40.50.410, no name defined]                                                                                                                                                                                         1jeyB02 B:243-443  [code=2.40.290.10, no name defined]                                                                                                                                                   1jeyB03 B:444-545  [code=1.10.1600.10, no name defined]                                                CATH domains
               Pfam domains ---Ku_N-1jeyB03 B:9-244                                                                                                                                                                                                                        ------Ku-1jeyB01 B:251-454                                                                                                                                                                                        ------------------Ku_C-1jeyB02 B:473-545                                                    Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhh......hhhhhhhhhhhhhhhhhhhh....eeeeeee.................eeeeeeee..hhhhhhhhhh.........hhhhhhhhhhhhhhhhh......eeeeeee..........hhhhhhhhhhhh.eeeeeee.....----------.................hhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhh.....hhhhh.....eeeeeee...eeeeeeeeeee.........eeee........eeeeeeeee......eehhh.eeeeeee..eeee.hhhhhhhhh......eeeeeeeee.hhhhhhhheeeeeeeeee...hhhhhhhhhhhhhhhhhh.eeeeeeee.......eeeeeeeee....eeeeeee..hhhh.................hhhhhhhhhhhhhhh..ee........ee..hhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhh.hhhhhhhhhhhhhhhhhhh..ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F--------------------------------------------V------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 2 (1) 2.Exon 2.5a  PDB: B:8-45 UniProt: 8-45  Exon 2.6b  PDB: B:46-107 UniProt: 46-107                      ---------------Exon 2.7c  PDB: B:123-164 UniProt: 123-164---------------------------------------------------------------Exon 2.9a  PDB: B:228-266              Exon 2.10a  PDB: B:267-313 UniProt: 267-313    -------------------------------------Exon 2.13            Exon 2.14  PDB: B:372-417 UniProt: 372-417    Exon 2.15  PDB: B:418-448      --------------------------------------------Exon 2.17  PDB: B:493-545 UniProt: 493-557            Transcript 2 (1)
           Transcript 2 (2) -----------------------------------------------------------------------------------------------------Exon 2.6g        ----------------------------------------Exon 2.8  PDB: B:164-228 (gaps) UniProt: 164-228                 ------------------------------------------------------------------------------------Exon 2.12  PDB: B:313-350             -------------------------------------------------------------------------------------------------Exon 2.16  PDB: B:448-492 UniProt: 448-492   ----------------------------------------------------- Transcript 2 (2)
                 1jey B   6 NKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLG----------GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAKKK 545
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165    |    -     | 185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545
                                                                                                                                                                                              170        181                                                                                                                                                                                                                                                                                                                                                                            

Chain C from PDB  Type:DNA  Length:18
                                                  
                 1jey C   1 GTTTTTAGTTTATTGGGC  18
                                    10        

Chain D from PDB  Type:DNA  Length:31
                                                               
                 1jey D   4 GCCCAGCTTTCCCAGCTAATAAACTAAAAAC  34
                                    13        23        33 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (4, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (4, 7)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Family: Ku (2)
1aKu-1jeyB01B:251-454
1bKu-1jeyA01A:261-463
(-)
Family: Ku_C (3)
2aKu_C-1jeyB02B:473-545
2bKu_C-1jeyA02A:469-534
(-)
Clan: vWA-like (60)

(-) Gene Ontology  (57, 95)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XRCC6_HUMAN | P12956)
molecular function
    GO:0051575    5'-deoxyribose-5-phosphate lyase activity    Catalysis of the beta-elimination of the 5' deoxyribose-5-phosphate at an abasic site in DNA where a DNA-(apurinic or apyrimidinic site) lyase has already cleaved the C-O-P bond 3' to the apurinic or apyrimidinic site.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004003    ATP-dependent DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0003691    double-stranded telomeric DNA binding    Interacting selectively and non-covalently with double-stranded telomere-associated DNA.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0044877    macromolecular complex binding    Interacting selectively and non-covalently with any macromolecular complex.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042162    telomeric DNA binding    Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0006266    DNA ligation    The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0071481    cellular response to X-ray    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).
    GO:0071480    cellular response to gamma radiation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0097680    double-strand break repair via classical nonhomologous end joining    An instance of double-strand break repair via nonhomologous end joining that requires a number of factors important for V(D)J recombination, including the KU70/80 heterodimer (KU), XRCC4, ligase IV, and DNA-PKcs in mammals. It does not produce translocations (as opposed to the alternative nonhomologous end joining).
    GO:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0075713    establishment of integrated proviral latency    A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0032481    positive regulation of type I interferon production    Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0051290    protein heterotetramerization    The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
    GO:0048660    regulation of smooth muscle cell proliferation    Any process that modulates the frequency, rate or extent of smooth muscle cell proliferation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0000723    telomere maintenance    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0043564    Ku70:Ku80 complex    Heterodimeric protein complex composed of a 70 kDa and a 80 kDa subunit, binds DNA through a channel formed by the heterodimer. Functions in DNA double stranded break repair, chromosome maintenance, transcription regulation, V(D)J recombination, and activation of DNA-PK.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0070419    nonhomologous end joining complex    A protein complex that plays a role in DNA double-strand break repair via nonhomologous end joining. Such complexes typically contain a specialized DNA ligase (e.g. Lig4 in eukaryotes) and one or more proteins that bind to DNA ends.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000783    nuclear telomere cap complex    A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes a linear chromosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain B   (XRCC5_HUMAN | P13010)
molecular function
    GO:0051575    5'-deoxyribose-5-phosphate lyase activity    Catalysis of the beta-elimination of the 5' deoxyribose-5-phosphate at an abasic site in DNA where a DNA-(apurinic or apyrimidinic site) lyase has already cleaved the C-O-P bond 3' to the apurinic or apyrimidinic site.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004003    ATP-dependent DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0003691    double-stranded telomeric DNA binding    Interacting selectively and non-covalently with double-stranded telomere-associated DNA.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016817    hydrolase activity, acting on acid anhydrides    Catalysis of the hydrolysis of any acid anhydride.
    GO:0044877    macromolecular complex binding    Interacting selectively and non-covalently with any macromolecular complex.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042162    telomeric DNA binding    Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0071481    cellular response to X-ray    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).
    GO:0071480    cellular response to gamma radiation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0006302    double-strand break repair    The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
    GO:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0075713    establishment of integrated proviral latency    A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
    GO:0060218    hematopoietic stem cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a hematopoietic stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
    GO:1904430    negative regulation of t-circle formation    Any process that stops, prevents or reduces the frequency, rate or extent of t-circle formation.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0050769    positive regulation of neurogenesis    Any process that activates or increases the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    GO:0032481    positive regulation of type I interferon production    Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0048660    regulation of smooth muscle cell proliferation    Any process that modulates the frequency, rate or extent of smooth muscle cell proliferation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0000723    telomere maintenance    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0043564    Ku70:Ku80 complex    Heterodimeric protein complex composed of a 70 kDa and a 80 kDa subunit, binds DNA through a channel formed by the heterodimer. Functions in DNA double stranded break repair, chromosome maintenance, transcription regulation, V(D)J recombination, and activation of DNA-PK.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0070419    nonhomologous end joining complex    A protein complex that plays a role in DNA double-strand break repair via nonhomologous end joining. Such complexes typically contain a specialized DNA ligase (e.g. Lig4 in eukaryotes) and one or more proteins that bind to DNA ends.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000783    nuclear telomere cap complex    A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes a linear chromosome.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        XRCC5_HUMAN | P130101jeq 1q2z 1rw2 3rz9
        XRCC6_HUMAN | P129561jeq 1jjr 3rzx

(-) Related Entries Specified in the PDB File

1jeq CRYSTAL STRUCTURE OF THE KU HETERODIMER