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 A NOVEL CHAPERONE COMPLEX FOR YEAST 20S PROTEASOME ASSEMBLY
 
Authors :  H. Yashiroda, T. Mizushima, K. Okamoto, T. Kameyama, H. Hayashi, T. Kishimoto, M. Kasahara, E. Kurimoto, E. Sakata, A. Suzuki, Y. Hirano, S. Murata, K. Kato, T. Yamane, K. Tanaka
Date :  03 Jul 07  (Deposition) - 22 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Proteasome, Chaperone, S. Cerevisiae (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yashiroda, T. Mizushima, K. Okamoto, T. Kameyama, H. Hayashi, T. Kishimoto, S. Niwa, M. Kasahara, E. Kurimoto, E. Sakata, K. Takagi, A. Suzuki, Y. Hirano, S. Murata, K. Kato, T. Yamane, K. Tanaka
Crystal Structure Of A Chaperone Complex That Contributes To The Assembly Of Yeast 20S Proteasomes
Nat. Struct. Mol. Biol. V. 15 228 2008
PubMed-ID: 18278057  |  Reference-DOI: 10.1038/NSMB.1386
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN YPL144W
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: DMP1
 
Molecule 2 - UNCHARACTERIZED PROTEIN YLR021W
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: DMP2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2Z5B)

(-) Sites  (0, 0)

(no "Site" information available for 2Z5B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z5B)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro B:11 -Lys B:12
2Leu B:125 -Pro B:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z5B)

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR021W1YLR021W.1XII:183622-184161540POC3_YEAST1-1791791B:1-178 (gaps)178
2.1YPL144W1YPL144W.1XVI:280479-280925447POC4_YEAST1-1481481A:1-147 (gaps)147

(-) 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:127
 aligned with POC4_YEAST | Q12245 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
           POC4_YEAST     1 MLVKTISRTIESESGFLQPTLDVIATLPADDRSKKIPISLVVGFKQEASLNSSSSLSCYYYAIPLMRDRHINLKSGGSNVVGIPLLDTKDDRIRDMARHMATIISERFNRPCYVTWSSLPSEDPSMLVANHLYILKKCLDLLKTELG 147
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains chaperone_DM     P-2z5bA01 A:1-143                                                                                                             ---- Pfam domains
         Sec.struct. author ..eeeeeeee..-----...eeeeeeee.........eeeeeee...-----..eeeeeeeeee...----------..eeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:1-147 (gaps) UniProt: 1-148 [INCOMPLETE]                                                                                           Transcript 2
                 2z5b A   1 MLVKTISRTIES-----QPTLDVIATLPADDRSKKIPISLVVGFKQE-----SSSLSCYYYAIPLMR----------SNVVGIPLLDTKDDRIRDMARHMATIISERFNRPCYVTWSSLPSEDPSMLVANHLYILKKCLDLLKTELG 147
                                    10 |     |20        30        40      |  -  |     60      |  -       |80        90       100       110       120       130       140       
                                      12    18                           47    53            67         78                                                                     


Chain B from PDB  Type:PROTEIN  Length:132
 aligned with POC3_YEAST | Q07951 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
           POC3_YEAST     1 MISYEFQTHLPKGKDSSLNASSENKELYVQATHFNNTILLQIRLNGEMDSTYEVSSKGLNPILDINVPLAGNLGNTGGDYDDEEEEFVRDHLSDYQVVTKLGDSADPKVPVVCVQIAELYRRVILPEVSGTMAQDNMQFSLLISMSSKIWRATKEQSADDNDFGKLVFVLKCIKDMYA 178
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains chaperone_DM          P-2z5bB01 B:1-174                                                                                                                                       ---- Pfam domains
         Sec.struct. author ..eeeeeee...----------...eeeeeeee....eeeeeee.....eeeeeee...--------------------...hhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhh....----------..eeeeee.hhhh------....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-178 (gaps) UniProt: 1-179 [INCOMPLETE]                                                                                                                          Transcript 1
                 2z5b B   1 MISYEFQTHLPK----------ENKELYVQATHFNNTILLQIRLNGEMDSTYEVSSKGL--------------------YDDEEEEFVRDHLSDYQVVTKLGDSADPKVPVVCVQIAELYRRVILPE----------QFSLLISMSSKIW------SADDNDFGKLVFVLKCIKDMYA 178
                                    10 |       -  |     30        40        50        |-         -        80        90       100       110       120      |  -       140       150      |160       170        
                                      12         23                                  59                   80                                            127        138         150    157
   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 2Z5B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z5B)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (6, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (POC4_YEAST | Q12245)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0051131    chaperone-mediated protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex, mediated by chaperone molecules that do not form part of the finished complex.
    GO:0043248    proteasome assembly    The aggregation, arrangement and bonding together of a mature, active proteasome complex.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Chain B   (POC3_YEAST | Q07951)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0051131    chaperone-mediated protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex, mediated by chaperone molecules that do not form part of the finished complex.
    GO:0070481    nuclear-transcribed mRNA catabolic process, non-stop decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.
    GO:0043248    proteasome assembly    The aggregation, arrangement and bonding together of a mature, active proteasome complex.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

 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 2z5b)
 
  Sites
(no "Sites" information available for 2z5b)
 
  Cis Peptide Bonds
    Leu B:125 - Pro B:126   [ RasMol ]  
    Pro B:11 - Lys B:12   [ 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
  2z5b
    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
  POC3_YEAST | Q07951
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  POC4_YEAST | Q12245
    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
  POC3_YEAST | Q07951
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  POC4_YEAST | Q12245
    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
        POC3_YEAST | Q07951: 2z5c
        POC4_YEAST | Q12245: 2z5c

(-) Related Entries Specified in the PDB File

2z5c COMPLEXED WITH DMP1, DMP2 AND PROTEASOME SUBUNIT ALPHA 5