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 :  MU2 ADAPTIN SUBUNIT OF THE AP2 ADAPTOR (C-TERMINAL DOMAIN) COMPLEXED WITH INTEGRIN ALPHA4 INTERNALISATION PEPTIDE QYKSILQE
 
Authors :  D. J. Owen, P. R. Evans, J. Ivaska
Date :  30 Nov 15  (Deposition) - 20 Jan 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.77
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Endocytosis, Clathrin Adaptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. De Franceschi, A. Arjonen, N. Elkhatib, K. Denessiouk, A. G. Wrobel, T. A. Wilson, J. Pouwels, G. Montagnac, D. J. Owen, J. Ivaska
Selective Integrin Endocytosis Is Driven By Alpha Chain:Ap2 Interactions
Nat. Struct. Mol. Biol. V. 23 172 2016
PubMed-ID: 26779610  |  Reference-DOI: 10.1038/NSMB.3161

(-) Compounds

Molecule 1 - AP-2 COMPLEX SUBUNIT MU
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLASMID
    Expression System Taxid: 562
    Fragment: INTERNALISATION SIGNAL BINDING DOMAIN
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: AP-2 MU CHAIN, ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT MU, ADAPTOR-RELATED PROTEIN COMPLEX 2 SUBUNIT MU, CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MU MEDIUM CHAIN, CLATHRIN COAT ASSEMBLY PROTEIN AP50, CLATHRIN COAT-ASSOCIATED PROTEIN AP50, HA2 50 KDA SUBUNIT, MU2- ADAPTIN, PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN
 
Molecule 2 - INTEGRIN ALPHA-4 SUBUNIT
    Chains: B
    Fragment: INTERNALISATION SIGNAL PEPTIDE, RESIDUES 150-157
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 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 5FPI)

(-) Sites  (0, 0)

(no "Site" information available for 5FPI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FPI)

(-) 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:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeeeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeee............eeee............ee....eeeeeeeeee.......eeeeeeeeee...eeeeeeeeee......eeeeeeeeee....eeeeeeee...eeeee....eeeeeeeeee...eeeeeeeeee.............eeeeeee........eeeeeee......hhhhheeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fpi A 159 IGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVKQSIAIDDCTFHQCVRLSKERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGIYETRC 435
                                   168       178       188       198       208       218  ||   244       254 ||    267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427        
                                                                                        221|               256|                                                                                                                                                                               
                                                                                         238                260                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..ee.. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5fpi B   1 QYKSIL   6
   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 5FPI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (55, 62)

Asymmetric/Biological Unit(hide GO term definitions)

 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 5fpi)
 
  Sites
(no "Sites" information available for 5fpi)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5fpi)
 

(-) 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
  5fpi
    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
  AP2M1_RAT | P84092
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  ITA4_HUMAN | P13612
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q8IU71_HUMAN | Q8IU71
    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
  AP2M1_RAT | P84092
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ITA4_HUMAN | P13612
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q8IU71_HUMAN | Q8IU71
    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
        AP2M1_RAT | P84092: 1bw8 1bxx 1h6e 1hes 1i31 2bp5 2jkr 2jkt 2pr9 2vgl 2xa7 3h85 3ml6 4uqi 5c7z
        ITA4_HUMAN | P13612: 3v4p 3v4v 4hkc 5c7z

(-) Related Entries Specified in the PDB File

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