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(-) Description

Title :  NMR SOLUTION STRUCTURE OF THE YEAST KINETOCHORE SPC24/SPC25 GLOBULAR DOMAIN
 
Authors :  J. R. Schnell, J. J. Chou
Date :  29 Jan 06  (Deposition) - 13 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Alpha-Beta, Complex, Coiled-Coil, Structural Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. R. Wei, J. R. Schnell, N. A. Larsen, P. K. Sorger, J. J. Chou, S. C. Harrison
Structure Of A Central Component Of The Yeast Kinetochore: The Spc24P/Spc25P Globular Domain.
Structure V. 6 1003 2006
PubMed-ID: 16765893  |  Reference-DOI: 10.1016/J.STR.2006.04.007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL 25.2 KDA PROTEIN IN AFG3-SEB2 INTERGENIC REGION
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: ROSETTA
    Expression System Plasmid: PET3ATR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SPC25P GLOBULAR DOMAIN
    Gene: YER018C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 2 - HYPOTHETICAL 24.6 KDA PROTEIN IN ILV2-ADE17 INTERGENIC REGION
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: ROSETTA
    Expression System Plasmid: PET3ATR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SPC24P GLOBULAR DOMAIN
    Gene: YMR117C, YM9718.16C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2FV4)

(-) Sites  (0, 0)

(no "Site" information available for 2FV4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FV4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FV4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FV4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FV4)

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YER018C1YER018C.1V:192623-191958666SPC25_YEAST1-2212211A:133-22189
2.1YMR117C1YMR117C.1XIII:501890-501249642SPC24_YEAST1-2132131B:156-21358

(-) Sequences/Alignments

NMR Structure
   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:89
 aligned with SPC25_YEAST | P40014 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:89
                                   142       152       162       172       182       192       202       212         
          SPC25_YEAST   133 NDAAEVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL 221
               SCOP domains d2fv4a1 A:133-221 Kinetochore protein Spc25                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhheeeeee.....eeeeee.....eeee...........ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:133-221 UniProt: 1-221 [INCOMPLETE]                                      Transcript 1
                 2fv4 A 133 NDAAEVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL 221
                                   142       152       162       172       182       192       202       212         


Chain B from PDB  Type:PROTEIN  Length:58
 aligned with SPC24_YEAST | Q04477 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:58
                                   165       175       185       195       205        
          SPC24_YEAST   156 NENILKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK 213
               SCOP domains d2fv4b1 B:156-213 Kinetochore protein Spc24                SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.eeee....eeeee......eeeee.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: B:156-213 UniProt: 1-213 [INCOMPLETE]       Transcript 2
                 2fv4 B 156 NENILKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK 213
                                   165       175       185       195       205
   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  (2, 2)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FV4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FV4)

(-) Gene Ontology  (15, 29)

NMR Structure(hide GO term definitions)
Chain A   (SPC25_YEAST | P40014)
molecular function
    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:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
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: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:0007020    microtubule nucleation    The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation).
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: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:0000778    condensed nuclear chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed nuclear chromosome and provides an attachment point for the spindle microtubules.
    GO:0000780    condensed nuclear chromosome, centromeric region    The region of a condensed nuclear chromosome that includes the centromere and associated proteins, including the kinetochore. 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: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.

Chain B   (SPC24_YEAST | Q04477)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
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: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:0007020    microtubule nucleation    The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation).
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: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:0000778    condensed nuclear chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed nuclear chromosome and provides an attachment point for the spindle microtubules.
    GO:0000780    condensed nuclear chromosome, centromeric region    The region of a condensed nuclear chromosome that includes the centromere and associated proteins, including the kinetochore. 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: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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  SPC24_YEAST | Q04477
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  SPC25_YEAST | P40014
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 Related Entries

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

UniProtKB/Swiss-Prot
        SPC24_YEAST | Q04477: 2ftx 4geq 5t6j 5tcs 5td8
        SPC25_YEAST | P40014: 2ftx 4geq 5t6j 5tcs 5td8

(-) Related Entries Specified in the PDB File

2ftx CRYSTAL STRUCTURE OF THE YEAST KINETOCHORE SPC24/SPC25 GLOBULAR DOMAIN