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 VPS75 HISTONE CHAPERONE
 
Authors :  Y. Tang, R. Marmorstein
Date :  30 Jun 08  (Deposition) - 09 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Vps75 (Vacuolar Protein Sorting 75), Nap1, Histone Chaperone, Nucleus, Phosphoprotein, Protein Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Tang, K. Meeth, E. Jiang, C. Luo, R. Marmorstein
Structure Of Vps75 And Implications For Histone Chaperone Function.
Proc. Natl. Acad. Sci. Usa V. 105 12206 2008
PubMed-ID: 18723682  |  Reference-DOI: 10.1073/PNAS.0802393105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PRSF-GST FUSION
    Expression System Strain: BL21(DE3) GOLD
    Expression System Vector Type: PLASMID
    Gene: VPS75, YNL246W, N0890
    Mutation: YES
    Organism Common: BREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3DM7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DM7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DM7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DM7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DM7)

(-) Exons   (0, 0)

(no "Exon" information available for 3DM7)

(-) 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:207
 aligned with VPS75_YEAST | P53853 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:214
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
          VPS75_YEAST    10 EHAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDL 223
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh.eeeeeeee.hhh........eeeeeee.........eeeeeeeeee.-------.eeee.......hhhhhhhh........hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dm7 A  10 EHAKAFLGLAKCEEEVDAIEREVELYRLNKmKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYmDTIDKIKVEWLALESEmYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKK-------GILTSEPVPIEWPQSYDSINPDLmKDKRSPEGKKKYRQGmKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDL 223
                                    19        29        39|       49        59        69        79|       89       |99       109       119       129       139       149       159|      169      |179       189       199       209       219    
                                                         40-MSE                                  80-MSE           97-MSE                         129     137                    160-MSE         176-MSE                                           


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with VPS75_YEAST | P53853 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:211
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 
          VPS75_YEAST    12 AKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRD 222
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhh.hhhhhhhhh.eeeeeeee.hhh........eeeeeee.........eeeeeeeeee.------..eeee.......hhhhhhhh........hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dm7 B  12 AKAFLGLAKCEEEVDAIEREVELYRLNKmKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYmDTIDKIKVEWLALESEmYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKK------DGILTSEPVPIEWPQSYDSINPDLmKDKRSPEGKKKYRQGmKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRD 222
                                    21        31        41        51        61        71        81        91     | 101       111       121       | -    |  141       151       161       171    |  181       191       201       211       221 
                                                       40-MSE                                  80-MSE           97-MSE                         129    136                     160-MSE         176-MSE
   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 3DM7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DM7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DM7)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VPS75_YEAST | P53853)
molecular function
    GO:0010698    acetyltransferase activator activity    Binds to and increases the activity of an acetyltransferase, an enzyme which catalyzes the transfer of an acetyl group to an acceptor molecule.
    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:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    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.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:2000617    positive regulation of histone H3-K9 acetylation    Any process that activates or increases the frequency, rate or extent of histone H3-K9 acetylation.
    GO:0035066    positive regulation of histone acetylation    Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to a histone protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3dm7)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3dm7)
 

(-) 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
  3dm7
    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
  VPS75_YEAST | P53853
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  VPS75_YEAST | P53853
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        VPS75_YEAST | P53853: 2zd7 3c9b 3c9d 3q33 3q35 3q66 3q68 5agc

(-) Related Entries Specified in the PDB File

3d35 CRYSTAL STRUCTURE OF RTT109 HISTONE ACETYLTRANSFERASE