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(-) Description

Title :  THE HETEROTRIMERIC COMPLEX OF KLUYVEROMYCES LACTIS SCM3, CSE4 AND H4
 
Authors :  U. S. Cho, S. C. Harrison
Date :  08 Apr 11  (Deposition) - 25 May 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Cell Cycle, Kinetochore, Centromere, Histone Chaperone, Budding Yeast (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. S. Cho, S. C. Harrison
Recognition Of The Centromere-Specific Histone Cse4 By The Chaperone Scm3.
Proc. Natl. Acad. Sci. Usa V. 108 9367 2011
PubMed-ID: 21606327  |  Reference-DOI: 10.1073/PNAS.1106389108

(-) Compounds

Molecule 1 - HISTONE H3-LIKE CENTROMERIC PROTEIN CSE4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 81-180
    Organism Scientific: KLUYVEROMYCES LACTIS NRRL Y-1140
    Organism Taxid: 284590
    Synonym: CENP-A HOMOLOG, CHROMOSOME SEGREGATION PROTEIN 4, CSE4
 
Molecule 2 - HISTONE H4
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 25-98
    Organism Scientific: KLUYVEROMYCES LACTIS NRRL Y-1140
    Organism Taxid: 284590
    Synonym: H4
 
Molecule 3 - SCM3
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 41-103
    Organism Scientific: KLUYVEROMYCES LACTIS NRRL Y-1140
    Organism Taxid: 284590
    Synonym: KLLA0F05115P

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1IOD2Ligand/IonIODIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2009BINDING SITE FOR RESIDUE IOD A1181
2AC2SOFTWARELYS B:31BINDING SITE FOR RESIDUE IOD A1182

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H3_2PS00959 Histone H3 signature 2.CENPA_KLULA112-120  1A:112-120

(-) Exons   (0, 0)

(no "Exon" information available for 2YFV)

(-) 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 A from PDB  Type:PROTEIN  Length:68
 aligned with CENPA_KLULA | Q6CTI2 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:73
                                   117       127       137       147       157       167       177   
          CENPA_KLULA   108 ISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRIR 180
               SCOP domains d2yfva_ A: automat     ed matches                                         SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains Histone-2yfvA01 A:     108-180                                            Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh..-----.eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----HISTONE_H------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 2yfv A 108 ISRMPFARLVKEVTDQFT-----LRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRIR 180
                                   117       | -   |   137       147       157       167       177   
                                           125   131                                                 


Chain B from PDB  Type:PROTEIN  Length:74
 aligned with Q6CMU6_KLULA | Q6CMU6 from UniProtKB/TrEMBL  Length:103

    Alignment length:74
                                    34        44        54        64        74        84        94    
         Q6CMU6_KLULA    25 DNIQGITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTL  98
               SCOP domains d2yfvb_ B: Histone H4                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains Histone-2yfvB01 B:24-93                                               ---- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 2yfv B  24 DNIQGITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTL  97
                                    33        43        53        63        73        83        93    


Chain C from PDB  Type:PROTEIN  Length:60
 aligned with Q6CL77_KLULA | Q6CL77 from UniProtKB/TrEMBL  Length:200

    Alignment length:60
                                    53        63        73        83        93       103
         Q6CL77_KLULA    44 VVYIMSKENRLIPKLSDEEVMERHKKADENMKRVWSQIIQKYESIDNQGDVIDLQTGEVI 103
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains -----------------Scm3-2yfvC01 C:61-103                       Pfam domains
         Sec.struct. author ..eee.....eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 2yfv C  44 VVYIMSKENRLIPKLSDEEVMERHKKADENMKRVWSQIIQKYESIDNQGDVIDLQTGEVI 103
                                    53        63        73        83        93       103
   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)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: Histone (49)
(-)
Clan: no clan defined [family: Scm3] (2)

(-) Gene Ontology  (24, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CENPA_KLULA | Q6CTI2)
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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    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.
biological process
    GO:0030543    2-micrometer plasmid partitioning    The process in which copies of the 2-micrometer plasmid, found in fungi such as Saccharomyces, are distributed to daughter cells upon cell division.
    GO:0000070    mitotic sister chromatid segregation    The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
cellular component
    GO:0043505    CENP-A containing nucleosome    A form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3).
    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: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:0005727    extrachromosomal circular DNA    Circular DNA structures that are not part of a 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:0000788    nuclear nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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   (Q6CMU6_KLULA | Q6CMU6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
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:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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 C   (Q6CL77_KLULA | Q6CL77)
molecular function
    GO:0097030    CENP-A containing nucleosome binding    Interacting selectively and non-covalently with a centromere-specific nucleosome, a form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3).
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
biological process
    GO:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    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:2000059    negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of protein ubiquitination involved in ubiquitin-dependent protein catabolic process.
    GO:0071459    protein localization to chromosome, centromeric region    Any process in which a protein is transported to, or maintained at, the centromeric region of a chromosome.
cellular component
    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: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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  2yfv
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 Related Entries

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

UniProtKB/Swiss-Prot
        CENPA_KLULA | Q6CTI2: 2yfw
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(-) Related Entries Specified in the PDB File

2yfw HETEROTETRAMER STRUCTURE OF KLUYVEROMYCES LACTIS CSE4,H4