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(-) Description

Title :  CRYSTAL STRUCTURE OF CENP-B(1-129) COMPLEXED WITH THE CENP-B BOX DNA
 
Authors :  Y. Tanaka, O. Nureki, H. Kurumizaka, S. Fukai, S. Kawaguchi, M. Ikuta, J. Iwahara, T. Okazaki, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  04 Dec 00  (Deposition) - 11 Jan 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Helix-Turn-Helix, Protein-Dna Complex, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Tanaka, O. Nureki, H. Kurumizaka, S. Fukai, S. Kawaguchi, M. Ikuta, J. Iwahara, T. Okazaki, S. Yokoyama
Crystal Structure Of The Cenp-B Protein-Dna Complex: The Dna-Binding Domains Of Cenp-B Induce Kinks In The Cenp-B Box Dna.
Embo J. V. 20 6612 2001
PubMed-ID: 11726497  |  Reference-DOI: 10.1093/EMBOJ/20.23.6612
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CENP-B BOX DNA
    ChainsB
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    SyntheticYES
 
Molecule 2 - CENP-B BOX DNA
    ChainsC
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    SyntheticYES
 
Molecule 3 - MAJOR CENTROMERE AUTOANTIGEN B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15D
    Expression System StrainJM109(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDNA BINDING DOMAIN
    GeneCENP-B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCENP-B

 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 1HLV)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_PSQPS50960 Psq-type HTH domain profile.CENPB_HUMAN1-52  1A:1-52
2HTH_CENPBPS51253 CENPB-type HTH domain profile.CENPB_HUMAN65-136  1A:65-129

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003797511ENSE00001482363chr20:3767337-37645002838CENPB_HUMAN1-6686681A:1-131131

(-) 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    
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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:131
 aligned with CENPB_HUMAN | P07199 from UniProtKB/Swiss-Prot  Length:599

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
          CENPB_HUMAN     1 MGPKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILASERKYGVASTCRKTNKLSPYDKLEGLLIAWFQQIRAAGLPVKGIILKEKALRIAEELGMDDFTASNGWLDRFRRRHG 131
               SCOP domains d1hlva1 A:1-66                                                    d1hlva2 A:67-131                                                  SCOP domains
               CATH domains --------1hlvA01 A:9-66 Homeodomain-like                           -----1hlvA02 A:72-131 Homeodomain-like                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_PSQ  PDB: A:1-52 UniProt: 1-52                  ------------HTH_CENPB  PDB: A:65-129 UniProt: 65-136                            PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-131 UniProt: 1-668 [INCOMPLETE]                                                                                  Transcript 1
                 1hlv A   1 MGPKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILASERKYGVASTCRKTNKLSPYDKLEGLLIAWFQQIRAAGLPVKGIILKEKALRIAEELGMDDFTASNGWLDRFRRRRS 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 

Chain B from PDB  Type:DNA  Length:21
                                                     
                 1hlv B   1 GCCTTCGTTGGAAACGGGATT  21
                                    10        20 

Chain C from PDB  Type:DNA  Length:21
                                                     
                 1hlv C   1 AATCCCGTTTCCAACGAAGGC  21
                                    10        20 

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CENPB_HUMAN | P07199)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0019237    centromeric DNA binding    Interacting selectively and non-covalently with a centromere, a region of chromosome where the spindle fibers attach during mitosis and meiosis.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0003696    satellite DNA binding    Interacting selectively and non-covalently with satellite DNA, the many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    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
        CENPB_HUMAN | P071991bw6 1ufi

(-) Related Entries Specified in the PDB File

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