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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN XLF
 
Authors :  S. N. Andres, M. S. Junop
Date :  12 Sep 07  (Deposition) - 01 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Xlf, Cernunnos, Non-Homologous End Joining, Dna Double Strand Break Repair, Alternative Splicing, Disease Mutation, Dna Damage, Dna Repair, Nucleus, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. N. Andres, M. Modesit, C. J. Tsai, G. Chu, M. S. Junop
Crystal Structure Of Human Xlf: A Twist In Nonhomologous Dna End-Joining
Mol. Cell V. 28 1093
PubMed-ID: 18158905  |  Reference-DOI: 10.1016/J.MOLCEL.2007.10.024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NON-HOMOLOGOUS END-JOINING FACTOR 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainROSSETTA(DE3)
    Expression System Taxid562
    FragmentN-TERMINAL FRAGMENT, UNP RESIDUES 1-224
    GeneNHEJ1, XLF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN CERNUNNOS, XRCC4-LIKE FACTOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 18)

Asymmetric/Biological Unit (1, 18)
No.NameCountTypeFull Name
1MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2R9A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R9A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R9A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038790A14TNHEJ1_HUMANPolymorphism34689457A/BA14T
2UniProtVAR_025704R57GNHEJ1_HUMANDisease (NHEJ1-SCID)118204451A/BR57G
3UniProtVAR_025705C123RNHEJ1_HUMANDisease (NHEJ1-SCID)118204452A/BC123R

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R9A)

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003568531bENSE00001869065chr2:220025575-220025442134NHEJ1_HUMAN-00--
1.4bENST000003568534bENSE00002167216chr2:220023084-220022908177NHEJ1_HUMAN1-59592A:1-59
B:1-59
59
59
1.5aENST000003568535aENSE00001708572chr2:220022406-220022194213NHEJ1_HUMAN60-130712A:60-130 (gaps)
B:60-130 (gaps)
71
71
1.6ENST000003568536ENSE00001664826chr2:220012517-220012379139NHEJ1_HUMAN131-177472A:131-177
B:131-177
47
47
1.7bENST000003568537bENSE00001631569chr2:220011460-22001140259NHEJ1_HUMAN177-196202A:177-196
B:177-196
20
20
1.11bENST0000035685311bENSE00001776599chr2:219942928-219942811118NHEJ1_HUMAN197-236402A:197-227
B:197-227
31
31
1.12ENST0000035685312ENSE00001706214chr2:219942086-219941968119NHEJ1_HUMAN236-275400--
1.13fENST0000035685313fENSE00001781266chr2:219941177-2199400431135NHEJ1_HUMAN276-299240--

(-) 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:219
 aligned with NHEJ1_HUMAN | Q9H9Q4 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
          NHEJ1_HUMAN     1 MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQ 227
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2r9aA01 A:2-141  [code=2.170.210.10, no name defined]                                                                                       -2r9aA02 A:143-227 Helix hairpin bin                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeee..eeeeeeeeee..eeeeeee....eeeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhh...--------.eeeeeee..eeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------T------------------------------------------G-----------------------------------------------------------------R-------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: A:1-59 UniProt: 1-59                       Exon 1.5a  PDB: A:60-130 (gaps) UniProt: 60-130                        Exon 1.6  PDB: A:131-177 UniProt: 131-177      -------------------Exon 1.11b  PDB: A:197-227      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7b           ------------------------------- Transcript 1 (2)
                 2r9a A   1 mEELEQGLLmQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLL--------ATFSCDCVADALILRVRSELSGLPFYWNFHCmLASPSLVSQHLIRPLmGmSLALQCQVRELATLLHmKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFmIEKLPEACSIGDGKPFVmNLQDLYmAVTTQHHH 227
                            |       10        20        30        40        50        60        70        80   |     -  |    100       110       120   |   130       140 |     150       160       170       180       190   |   200       210 |     220       
                            |       10-MSE                                                                    84       93                            124-MSE         140-MSE            159-MSE                            194-MSE           212-MSE  |        
                            1-MSE                                                                                                                                      142-MSE                                                                      219-MSE    

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with NHEJ1_HUMAN | Q9H9Q4 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
          NHEJ1_HUMAN     1 MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQ 227
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2r9aB01 B:2-141  [code=2.170.210.10, no name defined]                                                                                       -2r9aB02 B:143-227 Helix hairpin bin                                                   CATH domains
           Pfam domains (1) ----------XLF-2r9aB01 B:11-173                                                                                                                                               ------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------XLF-2r9aB02 B:11-173                                                                                                                                               ------------------------------------------------------ Pfam domains (2)
         Sec.struct. author hhhhhhhhhh...eeee....eeeeeeeee..eeeeeee....eeeeeeehhhhhhhhhhhh.....hhhhhhhhhhhh-------------.eeeeeee..eeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------T------------------------------------------G-----------------------------------------------------------------R-------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: B:1-59 UniProt: 1-59                       Exon 1.5a  PDB: B:60-130 (gaps) UniProt: 60-130                        Exon 1.6  PDB: B:131-177 UniProt: 131-177      -------------------Exon 1.11b  PDB: B:197-227      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7b           ------------------------------- Transcript 1 (2)
                 2r9a B   1 mEELEQGLLmQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNL-------------ATFSCDCVADALILRVRSELSGLPFYWNFHCmLASPSLVSQHLIRPLmGmSLALQCQVRELATLLHmKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFmIEKLPEACSIGDGKPFVmNLQDLYmAVTTQHHH 227
                            |       10        20        30        40        50        60        70        |-         -  |    100       110       120   |   130       140 |     150       160       170       180       190   |   200       210 |     220       
                            1-MSE   10-MSE                                                               79            93                            124-MSE         140-MSE            159-MSE                            194-MSE           212-MSE  |        
                                                                                                                                                                       142-MSE                                                                      219-MSE    

   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  (0, 0)

(no "SCOP Domain" information available for 2R9A)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Family: XLF (2)
1aXLF-2r9aB01B:11-173
1bXLF-2r9aB02B:11-173

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NHEJ1_HUMAN | Q9H9Q4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    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:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    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: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: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: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: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.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NHEJ1_HUMAN | Q9H9Q42qm4 3q4f 3rwr 3sr2 3w03

(-) Related Entries Specified in the PDB File

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