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(-) Description

Title :  MU2 ADAPTIN SUBUNIT (AP50) OF AP2 CLATHRIN ADAPTOR, COMPLEXED WITH EGFR INTERNALIZATION PEPTIDE FYRALM AT 2.5 A RESOLUTION
 
Authors :  Y. Modis, W. Boll, I. Rapoport, T. Kirchhausen
Date :  12 Feb 01  (Deposition) - 21 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,P
Keywords :  Beta-Sandwich, Peptide-Binding Site, Protein-Peptide Complex, Clathrin Adaptor, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Modis, W. Boll, I. Rapoport, T. Kirchhausen
Mu2 Adaptin Subunit (Ap50) Of Ap2 Clathrin Adaptor, Complexed With Egfr Internalization Peptide Fyralm At 2. 5 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLATHRIN COAT ASSEMBLY PROTEIN AP50
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPPROEX
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 122-435
    GeneAP50
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymMU2 ADAPTIN OF AP2 ADAPTOR
 
Molecule 2 - EPIDERMAL GROWTH FACTOR RECEPTOR
    ChainsP
    EngineeredYES
    FragmentRESIDUES 998-1003
    Other DetailsTHE HEXAPEPTIDE OF EPIDERMAL GROWTH FACTOR RECEPTOR WAS CHEMICALLY SYNTHESIZED
    SynonymEGFR
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AP

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1I31)

(-) Sites  (0, 0)

(no "Site" information available for 1I31)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I31)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I31)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I31)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CLAT_ADAPTOR_M_1PS00990 Clathrin adaptor complexes medium chain signature 1.AP2M1_RAT159-179  1A:159-179
2MHDPS51072 Mu homology domain (MHD) profile.AP2M1_RAT170-434  1A:170-434
3CLAT_ADAPTOR_M_2PS00991 Clathrin adaptor complexes medium chain signature 2.AP2M1_RAT263-277  1A:263-277

(-) Exons   (0, 0)

(no "Exon" information available for 1I31)

(-) 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:256
 aligned with AP2M1_RAT | P84092 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:277
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       
            AP2M1_RAT   159 IGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGIYETRC 435
               SCOP domains d1i31a_ A: Second domain of Mu2 adaptin subunit (ap50) of ap2                  adaptor                                                                                                                                                                                                SCOP domains
               CATH domains 1i31A02 A:159-284,A:392-430  [code=2.60.40.1170, no name defin                 ed]                                            1i31A01 A:285-391,A:431-433  [code=2.60.40.1170, no name defined]                                          1i31A02 A:159-284,A:392-430            1i3-- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeeeeeeee.....eeeeeeeeeeeeeee.....eeeeee....-----------------.......eeee.......----...eee....eeeeeeeeee.......eeeeeeeeee...eeeeeeeeee......eeeeeeeeee....eeeeeee....eeeeehhh.eeeeeeeeee...eeeeeeeeee.............eeeeeee........eeeeeee......hhhhheeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CLAT_ADAPTOR_M_1     -----------------------------------------------------------------------------------CLAT_ADAPTOR_M_-------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------MHD  PDB: A:170-434 UniProt: 170-434                                                                                                                                                                                                                                     - PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i31 A 159 IGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKI-----------------KQSIAIDDCTFHQCVRLS----ERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGIYETRC 435
                                   168       178       188       198       208       218 |       -       238       248      |  - |     268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       
                                                                                       220               238              255  260                                                                                                                                                                               

Chain P from PDB  Type:PROTEIN  Length:6
 aligned with A8IP97_RAT | A8IP97 from UniProtKB/TrEMBL  Length:234

    Alignment length:6
           A8IP97_RAT   139 FYRALM 144
               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
                 1i31 P   1 FYRALM   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I31)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AP2M1_RAT | P84092)
molecular function
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0050750    low-density lipoprotein particle receptor binding    Interacting selectively and non-covalently with a low-density lipoprotein receptor.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005048    signal sequence binding    Interacting selectively and non-covalently with a signal sequence, a specific peptide sequence found on protein precursors or mature proteins that dictates where the mature protein is localized.
biological process
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:1903077    negative regulation of protein localization to plasma membrane    Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to plasma membrane.
    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.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0030131    clathrin adaptor complex    A membrane coat adaptor complex that links clathrin to a membrane.
    GO:0030125    clathrin vesicle coat    A clathrin coat found on a vesicle.
    GO:0005905    clathrin-coated pit    A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043195    terminal bouton    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.
    GO:0030133    transport vesicle    Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

Chain P   (A8IP97_RAT | A8IP97)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
biological process
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AP2M1_RAT | P840921bw8 1bxx 1h6e 1hes 2bp5 2jkr 2jkt 2pr9 2vgl 2xa7 3h85 3ml6 4uqi 5c7z 5fpi
UniProtKB/TrEMBL
        A8IP97_RAT | A8IP971bw8

(-) Related Entries Specified in the PDB File

1bw8 MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH EGFR INTERNALIZATION PEPTIDE FYRALM
1bxx MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH TGN38 INTERNALIZATION PEPTIDE DYQRLN