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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIMERIZATION DOMAIN OF HUMAN CENP-B
 
Authors :  M. S. Tawaramoto, H. Kurumizaka, Y. Tanaka, S. -Y. Park, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 May 03  (Deposition) - 17 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Dimerization Domain, Salt Bridge, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Tawaramoto, S. -Y. Park, Y. Tanaka, O. Nureki, H. Kurumizaka, S. Yokoyama
Crystal Structure Of The Human Centromere Protein B (Cenp-B) Dimerization Domain At 1. 65-A Resolution
J. Biol. Chem. V. 278 51454 2003
PubMed-ID: 14522975  |  Reference-DOI: 10.1074/JBC.M310388200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MAJOR CENTROMERE AUTOANTIGEN B
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DIMERIZATION DOMAIN
    Gene: CENPB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CENP-B

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1UFI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UFI)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003797511ENSE00001482363chr20:3767337-37645002838CENPB_HUMAN1-6686684A:3-50
B:5-50
C:2-49
D:3-48		48
46
48
46

(-) Sequences/Alignments

Asymmetric 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:48
 aligned with CENPB_HUMAN | P07199 from UniProtKB/Swiss-Prot  Length:599

    Alignment length:48
                                   547       557       567       577        
          CENPB_HUMAN   538 EVPVPSFGEAMAYFAMVKRYLTSFPIDDRVQSHILHLEHDLVHVTRKN 585
               SCOP domains d1ufia_ A: Dimerisation domain of CENP-B         SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-50 UniProt: 1-668             Transcript 1
                 1ufi A   3 HMPVPSFGEAMAYFAMVKRYLTSFPIDDRVQSHILHLEHDLVHVTRKN  50
                                    12        22        32        42        


Chain B from PDB  Type:PROTEIN  Length:46
 aligned with CENPB_HUMAN | P07199 from UniProtKB/Swiss-Prot  Length:599

    Alignment length:46
                                   549       559       569       579      
          CENPB_HUMAN   540 PVPSFGEAMAYFAMVKRYLTSFPIDDRVQSHILHLEHDLVHVTRKN 585
               SCOP domains d1ufib_ B: Dimerisation domain of CENP-B       SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:5-50 UniProt: 1-668           Transcript 1
                 1ufi B   5 PVPSFGEAMAYFAMVKRYLTSFPIDDRVQSHILHLEHDLVHVTRKN  50
                                    14        24        34        44      


Chain C from PDB  Type:PROTEIN  Length:48
 aligned with CENPB_HUMAN | P07199 from UniProtKB/Swiss-Prot  Length:599

    Alignment length:48
                                   546       556       566       576        
          CENPB_HUMAN   537 DEVPVPSFGEAMAYFAMVKRYLTSFPIDDRVQSHILHLEHDLVHVTRK 584
               SCOP domains d1ufic_ C: Dimerisation domain of CENP-B         SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: C:2-49 UniProt: 1-668             Transcript 1
                 1ufi C   2 SHMPVPSFGEAMAYFAMVKRYLTSFPIDDRVQSHILHLEHDLVHVTRK  49
                                    11        21        31        41        


Chain D from PDB  Type:PROTEIN  Length:46
 aligned with CENPB_HUMAN | P07199 from UniProtKB/Swiss-Prot  Length:599

    Alignment length:46
                                   547       557       567       577      
          CENPB_HUMAN   538 EVPVPSFGEAMAYFAMVKRYLTSFPIDDRVQSHILHLEHDLVHVTR 583
               SCOP domains d1ufid_ D: Dimerisation domain of CENP-B       SCOP domains
               CATH domains ---------------------------------------------- CATH domains
           Pfam domains (1) --Cenp-B_dimeris-1ufiD01 D:5-48                Pfam domains (1)
           Pfam domains (2) --Cenp-B_dimeris-1ufiD02 D:5-48                Pfam domains (2)
           Pfam domains (3) --Cenp-B_dimeris-1ufiD03 D:5-48                Pfam domains (3)
           Pfam domains (4) --Cenp-B_dimeris-1ufiD04 D:5-48                Pfam domains (4)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:3-48 UniProt: 1-668           Transcript 1
                 1ufi D   3 HMPVPSFGEAMAYFAMVKRYLTSFPIDDRVQSHILHLEHDLVHVTR  48
                                    12        22        32        42
   Legend:   → Mismatch (orange background)
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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, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1UFI)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Cenp-B_dimeris] (1)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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

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        CENPB_HUMAN | P07199: 1bw6 1hlv

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