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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CHICKEN SPC24-SPC25 GLOBULAR DOMAIN IN COMPLEX WITH CENP-T PEPTIDE
 
Authors :  T. Nishino, T. Fukagawa
Date :  09 Oct 12  (Deposition) - 03 Apr 13  (Release) - 03 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  B,D,F  (1x)
Biol. Unit 2:  A,C,E  (1x)
Keywords :  Rwd Domain, Kinetochore Component, Chromosome Segregation, Ndc80 Complex, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Nishino, F. Rago, T. Hori, K. Tomii, I. M. Cheeseman, T. Fukagawa
Cenp-T Provides A Structural Platform For Outer Kinetochore Assembly
Embo J. V. 32 424 2013
PubMed-ID: 23334297  |  Reference-DOI: 10.1038/EMBOJ.2012.348

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    ChainsB, A
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRWD DOMAIN, GLOBULAR DOMAIN, UNP RESIDUES 132-234
    GeneSPC25
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    SynonymSPC25 PROTEIN
 
Molecule 2 - SPC24 PROTEIN
    ChainsD, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRWD DOMAIN, GLOBULAR DOMAIN
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
 
Molecule 3 - CENTROMERE PROTEIN T
    ChainsE, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCENP-T SPC24-25 INTERACTING REGION, RESIDUES 63-98
    GeneCENPT
    MutationYES
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    SynonymCENP-T

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x) B D F
Biological Unit 2 (1x)A C E 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3VZA)

(-) Sites  (0, 0)

(no "Site" information available for 3VZA)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VZA)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr B:195 -Pro B:196
2Thr A:195 -Pro A:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VZA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VZA)

(-) Exons   (0, 0)

(no "Exon" information available for 3VZA)

(-) 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:98
 aligned with E1C4Y2_CHICK | E1C4Y2 from UniProtKB/TrEMBL  Length:234

    Alignment length:98
                                   143       153       163       173       183       193       203       213       223        
         E1C4Y2_CHICK   134 RVERLCKSKELFEERLGLEIRRIHNEQLQFIFRHIDHKDPDKPYMFTLSINEQGDYEVTSCTPPLDCISEFQLKVRETNNFSAFIANIRKAFTALSFK 231
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhheeeeee...eeeeee...........eeeeeee.....eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3vza A 134 RVERLCKSKELFEERLGLEIRRIHNEQLQFIFRHIDHKDPDKPYMFTLSINEQGDYEVTSCTPPLDCISEFQLKVRETNNFSAFIANIRKAFTALSFK 231
                                   143       153       163       173       183       193       203       213       223        

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with E1C4Y2_CHICK | E1C4Y2 from UniProtKB/TrEMBL  Length:234

    Alignment length:99
                                   143       153       163       173       183       193       203       213       223         
         E1C4Y2_CHICK   134 RVERLCKSKELFEERLGLEIRRIHNEQLQFIFRHIDHKDPDKPYMFTLSINEQGDYEVTSCTPPLDCISEFQLKVRETNNFSAFIANIRKAFTALSFKQ 232
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhheeeeee...eeeeee...........eeeeeee.....eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3vza B 134 RVERLCKSKELFEERLGLEIRRIHNEQLQFIFRHIDHKDPDKPYMFTLSINEQGDYEVTSCTPPLDCISEFQLKVRETNNFSAFIANIRKAFTALSFKQ 232
                                   143       153       163       173       183       193       203       213       223         

Chain C from PDB  Type:PROTEIN  Length:62
 aligned with R4GRT4_CHICK | R4GRT4 from UniProtKB/TrEMBL  Length:73

    Alignment length:62
                                    21        31        41        51        61        71  
         R4GRT4_CHICK    12 AAYVTQLYYKISRIDWDYEVEPARIKGIHYGPDIAQPINMDSSHHSRCFISDYLWSLVPTAW  73
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhheee.......eeeeee......eeeeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 3vza C 134 AAYVTQLYYKISRIDWDYEVEPARIKGIHYGPDIAQPINMDSSHHSRCFISDYLWSLVPTAW 195
                                   143       153       163       173       183       193  

Chain D from PDB  Type:PROTEIN  Length:62
 aligned with R4GRT4_CHICK | R4GRT4 from UniProtKB/TrEMBL  Length:73

    Alignment length:62
                                    21        31        41        51        61        71  
         R4GRT4_CHICK    12 AAYVTQLYYKISRIDWDYEVEPARIKGIHYGPDIAQPINMDSSHHSRCFISDYLWSLVPTAW  73
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhheee.......eeeeee......eeeeee.hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 3vza D 134 AAYVTQLYYKISRIDWDYEVEPARIKGIHYGPDIAQPINMDSSHHSRCFISDYLWSLVPTAW 195
                                   143       153       163       173       183       193  

Chain E from PDB  Type:PROTEIN  Length:31
 aligned with CENPT_CHICK | F1NPG5 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:31
                                    72        82        92 
          CENPT_CHICK    63 NAFSELDNATPRVMLRKIIQNQPQVSPLALQ  93
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                 3vza E  63 NAFSELDSADPRVMLRRIIQNQPQVDPLALQ  93
                                    72        82        92 

Chain F from PDB  Type:PROTEIN  Length:31
 aligned with CENPT_CHICK | F1NPG5 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:31
                                    72        82        92 
          CENPT_CHICK    63 NAFSELDNATPRVMLRKIIQNQPQVSPLALQ  93
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                 3vza F  63 NAFSELDSADPRVMLRRIIQNQPQVDPLALQ  93
                                    72        82        92 

   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 3VZA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VZA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VZA)

(-) Gene Ontology  (16, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (E1C4Y2_CHICK | E1C4Y2)
biological process
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0007052    mitotic spindle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
cellular component
    GO:0031262    Ndc80 complex    A protein complex conserved among eukaryotes that forms part of the kinetochore and plays an essential role in forming stable kinetochore-microtubule attachments. The complex contains proteins known in several species, including budding and fission yeasts, as Ndc80p, Nuf2p, Spc24p, and Spc25p. In vertebrates it is part of the outer plate of the kinetochore.
    GO:0000777    condensed chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.

Chain C,D   (R4GRT4_CHICK | R4GRT4)

Chain E,F   (CENPT_CHICK | F1NPG5)
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).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    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: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:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0051382    kinetochore assembly    The aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
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:0000777    condensed chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
    GO:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    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
        CENPT_CHICK | F1NPG53b0c 3b0d 3vh5 3vh6
UniProtKB/TrEMBL
        E1C4Y2_CHICK | E1C4Y23vz9

(-) Related Entries Specified in the PDB File

3vz9