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
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ATG19 COILED-COIL COMPLEXED WITH APE1 PROPEPTIDE
 
Authors :  Y. Watanabe, N. N. Noda
Date :  20 Apr 16  (Deposition) - 29 Jun 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Receptor, Complex, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Yamasaki, Y. Watanabe, W. Adachi, K. Suzuki, K. Matoba, H. Kirisako H. Kumeta, H. Nakatogawa, Y. Ohsumi, F. Inagaki, N. N. Noda
Structural Basis For Receptor-Mediated Selective Autophagy Of Aminopeptidase I Aggregates
Cell Rep V. 16 19 2016
PubMed-ID: 27320913  |  Reference-DOI: 10.1016/J.CELREP.2016.05.066

(-) Compounds

Molecule 1 - AUTOPHAGY-RELATED PROTEIN 19
    Chains: A, B, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ATG19, CVT19, YOL082W, O0980, YOL01
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: CYTOPLASM-TO-VACUOLE TARGETING PROTEIN 19
 
Molecule 2 - APE1 PROPEPTIDE
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5JGE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JGE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JGE)

(-) 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:28
                                                            
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 5jge A 158 HMLDNFMKQLLKLEESLNKLELEQKVTN 185
                                   167       177        


Chain B from PDB  Type:PROTEIN  Length:27
                                                           
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                 5jge B 156 GPHMLDNFMKQLLKLEESLNKLELEQK 182
                                   165       175       


Chain C from PDB  Type:PROTEIN  Length:23
                                                       
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 5jge C  -1 GPMEEQREILEQLKKTLQMLTVY  21
                                     8        18   


Chain D from PDB  Type:PROTEIN  Length:30
                                                              
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 5jge D 156 GPHMLDNFMKQLLKLEESLNKLELEQKVTN 185
                                   165       175       185


Chain E from PDB  Type:PROTEIN  Length:30
                                                              
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 5jge E 156 GPHMLDNFMKQLLKLEESLNKLELEQKVTN 185
                                   165       175       185


Chain F from PDB  Type:PROTEIN  Length:23
                                                       
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 5jge F  -1 GPMEEQREILEQLKKTLQMLTVY  21
                                     8        18
   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 5JGE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 30)

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 5jge)
 
  Sites
(no "Sites" information available for 5jge)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5jge)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  5jge
    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
  ATG19_YEAST | P35193
    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
  AMPL_YEAST | P14904
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ATG19_YEAST | P35193
    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 5jgf 5jh9 5jhc 5jm9
        ATG19_YEAST | P35193: 2kzb 2zpn 5azf

(-) Related Entries Specified in the PDB File

5jgf