Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF S. CEREVESIAE MAPE1 DODECAMER
 
Authors :  C. Sachse, C. Bertipaglia
Date :  28 Apr 16  (Deposition) - 15 Jun 16  (Release) - 13 Jul 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  24.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Dodecamer, Aminopeptidase, Vacuole, Cvt, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bertipaglia, S. Schneider, A. J. Jakobi, A. K. Tarafder, Y. S. Bykov A. Picco, W. Kukulski, J. Kosinski, W. J. Hagen, A. C. Ravichandran, M. Wilmanns, M. Kaksonen, J. A. Briggs, C. Sachse
Higher-Order Assemblies Of Oligomeric Cargo Receptor Complexes Form The Membrane Scaffold Of The Cvt Vesicle.
Embo Rep. V. 17 1044 2016
PubMed-ID: 27266708  |  Reference-DOI: 10.15252/EMBR.201541960

(-) Compounds

Molecule 1 - VACUOLAR AMINOPEPTIDASE 1
    Chains: A
    EC Number: 3.4.11.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Expression System Variant: RIL
    Expression System Vector: PETM33
    Expression System Vector Type: PLASMID
    Gene: APE1, API, LAP4, YSC1, YKL103C, YKL455
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: AMINOPEPTIDASE YSCI,LEUCINE AMINOPEPTIDASE IV,LAPIV, LYSOSOMAL AMINOPEPTIDASE III,POLYPEPTIDASE,VACUOLAR AMINOPEPTIDASE I

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5JM9)

(-) Sites  (0, 0)

(no "Site" information available for 5JM9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JM9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:7 -Ile A:8
2Thr A:153 -Pro A:154
3Asp A:259 -Asp A:260

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JM9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JM9)

(-) Exons   (0, 0)

(no "Exon" information available for 5JM9)

(-) 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:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.hhhhhhhhhhhhhhh...ee...............eeeeeee...eeeeeee....hhhhh.eeeeee....eeeeeeeeeeeee..eeeeeeeee....hhhhh...eeeeeeeee........eeeeee..................ee....hhhhhh.......hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee...........hhhhhhhhhhhhhhhhhhh....hhhhhhhh.eeeee.........hhhhh...........eeeee........hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh.eeeeee..........eeee.hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jm9 A   3 HNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAKEDQTIPVEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFGEL 470
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 ||    184|      205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395      |412       422       432       442       452       462        
                                                                                                                                                                                           164|    184|                                                                                                                                                                                                           402|                                                            
                                                                                                                                                                                            177     196                                                                                                                                                                                                            410
   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 5JM9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JM9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JM9)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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 5jm9)
 
  Sites
(no "Sites" information available for 5jm9)
 
  Cis Peptide Bonds
    Asp A:259 - Asp A:260   [ RasMol ]  
    Asp A:7 - Ile A:8   [ RasMol ]  
    Thr A:153 - Pro A:154   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 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
  5jm9
    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
  AMPL_YEAST | P14904
    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)
  3.4.11.22
    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
  AMPL_YEAST | P14904
    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
        AMPL_YEAST | P14904: 4r8f 5jge 5jgf 5jh9 5jhc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5JM9)