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(-) Description

Title :  CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX
 
Authors :  B. L. Sibanda, S. E. Critchlow, J. Begun, X. Y. Pei, S. P. Jackson, T. L. Blundell, L. Pellegrini
Date :  03 May 01  (Deposition) - 21 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna End Joining, Double-Strand Break Repair, V(D)J Recombination, Protein-Protein Complex, Coiled Coil, Gene Regulation/Ligase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. L. Sibanda, S. E. Critchlow, J. Begun, X. Y. Pei, S. P. Jackson, T. L. Blundell, L. Pellegrini
Crystal Structure Of An Xrcc4-Dna Ligase Iv Complex.
Nat. Struct. Biol. V. 8 1015 2001
PubMed-ID: 11702069  |  Reference-DOI: 10.1038/NSB725
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA REPAIR PROTEIN XRCC4
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET15A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentXRCC4 FRAGMENT, RESIDUES 1-213
    GeneXRCC4
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - DNA LIGASE IV
    ChainsC
    EC Number6.5.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPTYB3
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentLINKER CONNECTING BRCT DOMAINS, RESIDUES 748-784
    GeneLIG4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPOLYDEOXYRIBONUCLEOTIDE SYNTHASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1IK9)

(-) Sites  (0, 0)

(no "Site" information available for 1IK9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IK9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IK9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 13)

Asymmetric/Biological Unit (7, 13)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_022310S12CXRCC4_HUMANPolymorphism28383138A/BS12C
2UniProtVAR_075822W43RXRCC4_HUMANDisease (SSMED)587779351A/BW43R
3UniProtVAR_022311A56TXRCC4_HUMANPolymorphism28383151A/BA56T
4UniProtVAR_022312I134TXRCC4_HUMANPolymorphism28360135A/BI134T
5UniProtVAR_022313E142QXRCC4_HUMANPolymorphism28360136A/BE142Q
6UniProtVAR_075823R161QXRCC4_HUMANDisease (SSMED)797045017A/BR161Q
7UniProtVAR_075826L774PDNLI4_HUMANUnclassified  ---CL774P

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IK9)

(-) Exons   (5, 9)

Asymmetric/Biological Unit (5, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003386351bENSE00001556292chr5:82373346-8237343489XRCC4_HUMAN-00--
1.2bENST000003386352bENSE00002174590chr5:82400729-82400877149XRCC4_HUMAN1-47472A:1-47
B:1-47
47
47
1.3aENST000003386353aENSE00000971597chr5:82406847-82407022176XRCC4_HUMAN47-105592A:47-105 (gaps)
B:47-105 (gaps)
59
59
1.4ENST000003386354ENSE00001005114chr5:82491589-82491755167XRCC4_HUMAN106-161562A:106-161
B:106-161
56
56
1.5ENST000003386355ENSE00001005109chr5:82499371-82499526156XRCC4_HUMAN161-213532A:161-211
B:161-201
51
41
1.6ENST000003386356ENSE00001005110chr5:82500634-82500740107XRCC4_HUMAN213-249370--
1.7aENST000003386357aENSE00001005113chr5:82554349-82554496148XRCC4_HUMAN249-298500--
1.8aENST000003386358aENSE00001932573chr5:82648944-82649530587XRCC4_HUMAN298-336390--

2.3ENST000003569223ENSE00001263649chr13:108867130-108866886245DNLI4_HUMAN-00--
2.4bENST000003569224bENSE00001930844chr13:108863644-1088605653080DNLI4_HUMAN1-9219211C:755-78228

(-) 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:207
 aligned with XRCC4_HUMAN | Q13426 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
          XRCC4_HUMAN     1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFILVLNEKKTKIRSLHNKLLNAAQEREKDIKQ 211
               SCOP domains d1ik9a1 A:1-117 XRCC4, N-terminal domain                                                                             d1ik9a2 A:118-211 XRCC4, C-terminal oligomerization domain                                     SCOP domains
               CATH domains 1ik9A01 A:1-118  [code=2.170.210.10, no name defined]                                                                 1ik9A02 A:119-211  [code=1.20.5.370, no name defined]                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..eeeeeeeeeeee..hhh.eeeeeee....eeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhh.----...eeeee.....eeeeeee....eeeeeeee.ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------C------------------------------R------------T-----------------------------------------------------------------------------T-------Q------------------Q-------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:1-47 UniProt: 1-47           ----------------------------------------------------------Exon 1.4  PDB: A:106-161 UniProt: 106-161               -------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.3a  PDB: A:47-105 (gaps) UniProt: 47-105            -------------------------------------------------------Exon 1.5  PDB: A:161-211 UniProt: 161-213           Transcript 1 (2)
                 1ik9 A   1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLS----ADVYTFNFSKESAYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELIAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETDLYKRFILVLNEKKTKIRSLHNKLLNAAQEREKDIKQ 211
                                    10        20        30        40        50        60        70     |   -|       90       100       110       120       130       140       150       160       170       180       190       200       210 
                                                                                                      76   81                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:195
 aligned with XRCC4_HUMAN | Q13426 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
          XRCC4_HUMAN     1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFILVLNEKKTKIRSLHNKLLNA 201
               SCOP domains d1ik9b1 B:1-117 XRCC4, N-terminal domain                                                                             d1ik9b2 B:118-201 XRCC4, C-terminal oligomerization domain                           SCOP domains
               CATH domains 1ik9B01 B:1-118  [code=2.170.210.10, no name defined]                                                                 1ik9B02 B:119-201  [code=1.20.5.370, no name defined]                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeeeee..hhh.eeeeeee....eeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhh.------.eeeee.....eeeeeeee..eeeeeeeee.ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------C------------------------------R------------T-----------------------------------------------------------------------------T-------Q------------------Q---------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: B:1-47 UniProt: 1-47           ----------------------------------------------------------Exon 1.4  PDB: B:106-161 UniProt: 106-161               ---------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.3a  PDB: B:47-105 (gaps) UniProt: 47-105            -------------------------------------------------------Exon 1.5  PDB: B:161-201 UniProt: 161-213 Transcript 1 (2)
                 1ik9 B   1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLS------VYTFNFSKESAYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELIAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETDLYKRFILVLNEKKTKIRSLHNKLLNA 201
                                    10        20        30        40        50        60        70     |   -  |     90       100       110       120       130       140       150       160       170       180       190       200 
                                                                                                      76     83                                                                                                                      

Chain C from PDB  Type:PROTEIN  Length:28
 aligned with DNLI4_HUMAN | P49917 from UniProtKB/Swiss-Prot  Length:911

    Alignment length:28
                                   764       774        
          DNLI4_HUMAN   755 AREYDCYGDSYFIDTDLNQLKEVFSGIK 782
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------P-------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
               Transcript 2 Exon 2.4b  PDB: C:755-782    Transcript 2
                 1ik9 C 755 AREYDCYGDSYFIDTDLNQLKEVFSGIK 782
                                   764       774        

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IK9)

(-) Gene Ontology  (61, 80)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (XRCC4_HUMAN | Q13426)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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).
biological process
    GO:0051103    DNA ligation involved in DNA repair    The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair.
    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:0071285    cellular response to lithium ion    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 lithium (Li+) ion stimulus.
    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:0051351    positive regulation of ligase activity    Any process that activates or increases the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    GO:0010165    response to X-ray    Any process that results in a change in state or activity of a cell or an organism (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).
cellular component
    GO:0032807    DNA ligase IV complex    A eukaryotically conserved protein complex that contains DNA ligase IV and is involved in DNA repair by non-homologous end joining; in addition to the ligase, the complex also contains XRCC4 or a homolog, e.g. Saccharomyces Lif1p.
    GO:0005958    DNA-dependent protein kinase-DNA ligase 4 complex    A large protein complex which is involved in the repair of DNA double-strand breaks and, in mammals, V(D)J recombination events. It consists of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), the DNA end-binding heterodimer Ku, the nuclear phosphoprotein XRCC4 or a homolog thereof, and DNA ligase IV.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0000793    condensed chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
    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: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: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.

Chain C   (DNLI4_HUMAN | P49917)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003910    DNA ligase (ATP) activity    Catalysis of the reaction: ATP + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + diphosphate + deoxyribonucleotide(n+m).
    GO:0003909    DNA ligase activity    Catalysis of the formation of a phosphodiester bond between the 3'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of another. This reaction requires an energy source such as ATP or NAD+.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006266    DNA ligation    The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
    GO:0051102    DNA ligation involved in DNA recombination    The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA recombination.
    GO:0051103    DNA ligation involved in DNA repair    The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair.
    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:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0033077    T cell differentiation in thymus    The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus.
    GO:0033153    T cell receptor V(D)J recombination    The process in which T cell receptor V, D, and J, or V and J gene segments, depending on the specific locus, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).
    GO:0033151    V(D)J recombination    The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    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:0071285    cellular response to lithium ion    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 lithium (Li+) ion stimulus.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0051276    chromosome organization    A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
    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: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:0033152    immunoglobulin V(D)J recombination    The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0045190    isotype switching    The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus.
    GO:0006273    lagging strand elongation    The synthesis of DNA from a template strand in a net 3' to 5' direction. Lagging strand DNA elongation proceeds by discontinuous synthesis of short stretches of DNA, known as Okazaki fragments, from RNA primers; these fragments are then joined by DNA ligase. Although each segment of nascent DNA is synthesized in the 5' to 3' direction, the overall direction of lagging strand synthesis is 3' to 5', mirroring the progress of the replication fork.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    GO:0006297    nucleotide-excision repair, DNA gap filling    Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.
    GO:2001252    positive regulation of chromosome organization    Any process that activates or increases the frequency, rate or extent of chromosome organization.
    GO:0048146    positive regulation of fibroblast proliferation    Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
    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:0002328    pro-B cell differentiation    The process in which a precursor cell type acquires the specialized features of a pro-B cell. Pro-B cells are the earliest stage of the B cell lineage and undergo heavy chain D and J gene rearrangements, although they are not fully committed.
    GO:0010165    response to X-ray    Any process that results in a change in state or activity of a cell or an organism (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:0010332    response to gamma radiation    Any process that results in a change in state or activity of a cell or an organism (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:0010212    response to ionizing radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
    GO:0000012    single strand break repair    The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair.
    GO:0035019    somatic stem cell population maintenance    Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
cellular component
    GO:0032807    DNA ligase IV complex    A eukaryotically conserved protein complex that contains DNA ligase IV and is involved in DNA repair by non-homologous end joining; in addition to the ligase, the complex also contains XRCC4 or a homolog, e.g. Saccharomyces Lif1p.
    GO:0005958    DNA-dependent protein kinase-DNA ligase 4 complex    A large protein complex which is involved in the repair of DNA double-strand breaks and, in mammals, V(D)J recombination events. It consists of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), the DNA end-binding heterodimer Ku, the nuclear phosphoprotein XRCC4 or a homolog thereof, and DNA ligase IV.
    GO:0000793    condensed chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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: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

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        DNLI4_HUMAN | P499172e2w 3ii6 3vnn 3w1b 3w1g 3w5o 4hto 4htp
        XRCC4_HUMAN | Q134261fu1 3ii6 3mud 3q4f 3rwr 3sr2 3w03 4xa4 5chx 5cj0 5cj4 5e50

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