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(-) Description

Title :  HETEROTETRAMER STRUCTURE OF KLUYVEROMYCES LACTIS CSE4,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 :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,G,H  (1x)
Biol. Unit 2:  C,D,E,F  (1x)
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, C, E, G
    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: HISTONE-FOLD DOMAIN, RESIDUES 93-184
    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, D, F, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: KLUYVEROMYCES LACTIS NRRL Y-1140
    Organism Taxid: 284590
    Synonym: H4

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB    GH
Biological Unit 2 (1x):   CDEF  

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2YFW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H3_2PS00959 Histone H3 signature 2.CENPA_KLULA112-120
 
 
 		  4A:112-120
C:112-120
E:112-120
G:112-120
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H3_2PS00959 Histone H3 signature 2.CENPA_KLULA112-120
 
 
 		  2A:112-120
-
-
G:112-120
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H3_2PS00959 Histone H3 signature 2.CENPA_KLULA112-120
 
 
 		  2-
C:112-120
E:112-120
-

(-) Exons   (0, 0)

(no "Exon" information available for 2YFW)

(-) 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:78
 aligned with CENPA_KLULA | Q6CTI2 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:79
                                   114       124       134       144       154       164       174         
          CENPA_KLULA   105 DLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRIRGQF 183
               SCOP domains d2yfwa_ A: automated ma tches                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh..-...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------HISTONE_H--------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 2yfw A 105 DLLISRMPFARLVKEVTDQFTTE-EPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRIRGQF 183
                                   114       124  | |  134       144       154       164       174         
                                                127 |                                                      
                                                  129                                                      


Chain B from PDB  Type:PROTEIN  Length:66
 aligned with Q6CMU6_KLULA | Q6CMU6 from UniProtKB/TrEMBL  Length:103

    Alignment length:66
                                    39        49        59        69        79        89      
         Q6CMU6_KLULA    30 ITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQG  95
               SCOP domains d2yfwb_ B: automated matches                                       SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 2yfw B  29 ITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQG  94
                                    38        48        58        68        78        88      


Chain C from PDB  Type:PROTEIN  Length:71
 aligned with CENPA_KLULA | Q6CTI2 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:78
                                   113       123       133       143       153       163       173        
          CENPA_KLULA   104 TDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRIRG 181
               SCOP domains d2yfwc_ C: automated        matches                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh.-------.eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------HISTONE_H------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 2yfw C 104 TDLLISRMPFARLVKEVTDQ-------LRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRIRG 181
                                   113       123       133       143       153       163       173        
                                             123     131                                                  


Chain D from PDB  Type:PROTEIN  Length:71
 aligned with Q6CMU6_KLULA | Q6CMU6 from UniProtKB/TrEMBL  Length:103

    Alignment length:71
                                    34        44        54        64        74        84        94 
         Q6CMU6_KLULA    25 DNIQGITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQG  95
               SCOP domains d2yfwd_ D: automated matches                                            SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 2yfw D  24 DNIQGITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQG  94
                                    33        43        53        63        73        83        93 


Chain E from PDB  Type:PROTEIN  Length:88
 aligned with CENPA_KLULA | Q6CTI2 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:92
                                   102       112       122       132       142       152       162       172       182  
          CENPA_KLULA    93 ALAEIRKYQRSTDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRIRGQFI 184
               SCOP domains d2yfwe_ E: automated matches                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh......hhhhhhhhhhhhhh...----..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------HISTONE_H---------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2yfw E  93 ALAEIRKYQRSTDLLISRMPFARLVKEVTDQFT----PLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRIRGQFI 184
                                   102       112       122  |    132       142       152       162       172       182  
                                                          125  130                                                      


Chain F from PDB  Type:PROTEIN  Length:72
 aligned with Q6CMU6_KLULA | Q6CMU6 from UniProtKB/TrEMBL  Length:103

    Alignment length:72
                                    33        43        53        63        73        83        93  
         Q6CMU6_KLULA    24 RDNIQGITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQG  95
               SCOP domains d2yfwf_ F: automated matches                                             SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 2yfw F  23 RDNIQGITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQG  94
                                    32        42        52        62        72        82        92  


Chain G from PDB  Type:PROTEIN  Length:78
 aligned with CENPA_KLULA | Q6CTI2 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:78
                                   113       123       133       143       153       163       173        
          CENPA_KLULA   104 TDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRIRG 181
               SCOP domains d2yfwg_ G: automated matches                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Histone-2yfwG01 G:104-180                                                    - Pfam domains (1)
           Pfam domains (2) Histone-2yfwG02 G:104-180                                                    - Pfam domains (2)
           Pfam domains (3) Histone-2yfwG03 G:104-180                                                    - Pfam domains (3)
           Pfam domains (4) Histone-2yfwG04 G:104-180                                                    - Pfam domains (4)
         Sec.struct. author .....hhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------HISTONE_H------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 2yfw G 104 TDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRIRG 181
                                   113       123       133       143       153       163       173        


Chain H from PDB  Type:PROTEIN  Length:80
 aligned with Q6CMU6_KLULA | Q6CMU6 from UniProtKB/TrEMBL  Length:103

    Alignment length:80
                                    33        43        53        63        73        83        93       103
         Q6CMU6_KLULA    24 RDNIQGITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG 103
               SCOP domains d2yfwh_ H: automated matches                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Histone-2yfwH01 H:24-93                                               --------- Pfam domains (1)
           Pfam domains (2) -Histone-2yfwH02 H:24-93                                               --------- Pfam domains (2)
           Pfam domains (3) -Histone-2yfwH03 H:24-93                                               --------- Pfam domains (3)
           Pfam domains (4) -Histone-2yfwH04 H:24-93                                               --------- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 2yfw H  23 RDNIQGITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG 102
                                    32        42        52        62        72        82        92       102
   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  (1, 8)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 8)

Asymmetric Unit
(-)
Clan: Histone (49)

(-) Gene Ontology  (17, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G   (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,D,F,H   (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.

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  2yfw
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 Related Entries

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

UniProtKB/Swiss-Prot
        CENPA_KLULA | Q6CTI2: 2yfv
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        Q6CMU6_KLULA | Q6CMU6: 2yfv

(-) Related Entries Specified in the PDB File

2yfv THE HETEROTRIMERIC COMPLEX OF KLUYVEROMYCES LACTIS SCM3, CSE4,AND H4