Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE CHICKEN SPC24-SPC25 GLOBULAR DOMAIN
 
Authors :  T. Nishino, T. Fukagawa
Date :  09 Oct 12  (Deposition) - 03 Apr 13  (Release) - 03 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.03
Chains :  Asym./Biol. Unit :  B,D
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
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RWD DOMAIN, GLOBULAR DOMAIN, UNP RESIDUES 131-234
    Gene: SPC25
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Synonym: SPC25 PROTEIN
 
Molecule 2 - SPC24 PROTEIN
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RWD DOMAIN, GLOBULAR DOMAIN
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : BD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3VZ9)

(-) Sites  (0, 0)

(no "Site" information available for 3VZ9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VZ9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr B:195 -Pro B:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VZ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VZ9)

(-) Exons   (0, 0)

(no "Exon" information available for 3VZ9)

(-) 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 B from PDB  Type:PROTEIN  Length:103
 aligned with E1C4Y2_CHICK | E1C4Y2 from UniProtKB/TrEMBL  Length:234

    Alignment length:103
                                   140       150       160       170       180       190       200       210       220       230   
         E1C4Y2_CHICK   131 TKERVERLCKSKELFEERLGLEIRRIHNEQLQFIFRHIDHKDPDKPYMFTLSINEQGDYEVTSCTPPLDCISEFQLKVRETNNFSAFIANIRKAFTALSFKQS 233
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhheeeeee...eeeeee...........eeeeeee.....eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3vz9 B 131 TKERVERLCKSKELFEERLGLEIRRIHNEQLQFIFRHIDHKDPDKPYMFTLSINEQGDYEVTSCTPPLDCISEFQLKVRETNNFSAFIANIRKAFTALSFKQS 233
                                   140       150       160       170       180       190       200       210       220       230   


Chain D from PDB  Type:PROTEIN  Length:60
 aligned with R4GRT3_CHICK | R4GRT3 from UniProtKB/TrEMBL  Length:73

    Alignment length:60
                                    23        33        43        53        63        73
         R4GRT3_CHICK    14 YVTQLYYKISRIDWDYEVEPARIKGIHYGPDIAQPINMDSSHHSRCFISDYLWSLVPTAW  73
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhheee.......eeeeee......eeeeee....hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 3vz9 D 136 YVTQLYYKISRIDWDYEVEPARIKGIHYGPDIAQPINMDSSHHSRCFISDYLWSLVPTAW 195
                                   145       155       165       175       185       195
   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 3VZ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VZ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VZ9)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain 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 D   (R4GRT3_CHICK | R4GRT3)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3vz9)
 
  Sites
(no "Sites" information available for 3vz9)
 
  Cis Peptide Bonds
    Thr B:195 - Pro B:196   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3vz9
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  E1C4Y2_CHICK | E1C4Y2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  R4GRT3_CHICK | R4GRT3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  E1C4Y2_CHICK | E1C4Y2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  R4GRT3_CHICK | R4GRT3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        E1C4Y2_CHICK | E1C4Y2: 3vza

(-) Related Entries Specified in the PDB File

3vza