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(-) Description

Title :  GAMMA-ADAPTIN APPENDAGE DOMAIN FROM CLATHRIN ADAPTOR AP1 A753D MUTANT
 
Authors :  P. R. Evans, A. E. Miele, D. J. Owen, H. M. Mcmahon, H. M. Kent
Date :  30 Apr 02  (Deposition) - 22 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Endocytosis, Adaptor, Coated Pits (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. M. Kent, H. M. Mcmahon, P. R. Evans, A. Benmerah, D. J. Owen
Gamma-Adaptin Appendage Domain. Structure And Binding Site For Eps15 And Gamma-Synergin
Structure V. 10 1139 2002
PubMed-ID: 12176391  |  Reference-DOI: 10.1016/S0969-2126(02)00801-8

(-) Compounds

Molecule 1 - ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX 4T2
    Expression System StrainDH5ALPHA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentAPPENDAGE DOMAIN, RESIDUES 694-821
    MutationYES
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymGAMMA-ADAPTIN, GOLGI ADAPTOR HA1/AP1 ADAPTIN GAMMA SUBUNIT, CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 GAMMA LARGE CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:708 , ASN A:815 , THR B:708BINDING SITE FOR RESIDUE CL A1823

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAEPS50180 Gamma-adaptin ear (GAE) domain profile.AP1G1_MOUSE702-817
 
  2A:702-817
B:702-817
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAEPS50180 Gamma-adaptin ear (GAE) domain profile.AP1G1_MOUSE702-817
 
  1A:702-817
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAEPS50180 Gamma-adaptin ear (GAE) domain profile.AP1G1_MOUSE702-817
 
  1-
B:702-817

(-) Exons   (0, 0)

(no "Exon" information available for 1GYW)

(-) 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:126
 aligned with AP1G1_MOUSE | P22892 from UniProtKB/Swiss-Prot  Length:822

    Alignment length:126
                                   706       716       726       736       746       756       766       776       786       796       806       816      
          AP1G1_MOUSE   697 FNDIAPGIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ 822
               SCOP domains d1gywa_ A: Gamma1-adaptin domain                                                                                               SCOP domains
               CATH domains 1gywA00 A:697-822  [code=2.60.40.1230, no name defined]                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeee..eeeeeeeee......eeeeeeeeee......eeeeeeee.....eeee........hhhhh..eeeeeeee........eeeeeeeee..eeeeeeeee...hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----GAE  PDB: A:702-817 UniProt: 702-817                                                                                ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gyw A 697 FNDIAPGIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQADVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ 822
                                   706       716       726       736       746       756       766       776       786       796       806       816      

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with AP1G1_MOUSE | P22892 from UniProtKB/Swiss-Prot  Length:822

    Alignment length:128
                                   704       714       724       734       744       754       764       774       784       794       804       814        
          AP1G1_MOUSE   695 PLFNDIAPGIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ 822
               SCOP domains d1gywb_ B: Gamma1-adaptin domain                                                                                                 SCOP domains
               CATH domains 1gywB00 B:695-822  [code=2.60.40.1230, no name defined]                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee..eeeeeeeee......eeeeeeeeee......eeeeeeee.....eeee........hhhhh..eeeeeeee........eeeeeeeee..eeeeeeeee...hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------GAE  PDB: B:702-817 UniProt: 702-817                                                                                ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gyw B 695 PLFNDIAPGIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQADVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ 822
                                   704       714       724       734       744       754       764       774       784       794       804       814        

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (AP1G1_MOUSE | P22892)
molecular function
    GO:0030742    GTP-dependent 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) using energy from the hydrolysis of GTP.
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0019894    kinesin binding    Interacting selectively and non-covalently and stoichiometrically with kinesin, a member of a superfamily of microtubule-based motor proteins that perform force-generating tasks such as organelle transport and chromosome segregation.
    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:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    GO:0090160    Golgi to lysosome transport    The directed movement of substances from the Golgi to lysosomes.
    GO:0035646    endosome to melanosome transport    The directed movement of substances from endosomes to the melanosome, a specialised lysosome-related organelle.
    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:0043323    positive regulation of natural killer cell degranulation    Any process that activates or increases the frequency, rate or extent of natural killer cell degranulation.
    GO:0045954    positive regulation of natural killer cell mediated cytotoxicity    Any process that activates or increases the frequency, rate or extent of natural killer cell mediated cytotoxicity.
    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:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0030131    clathrin adaptor complex    A membrane coat adaptor complex that links clathrin to a membrane.
    GO:0030136    clathrin-coated vesicle    A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes.
    GO:0030665    clathrin-coated vesicle membrane    The lipid bilayer surrounding a clathrin-coated vesicle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030117    membrane coat    Any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes, and possibly others. They are found associated with membranes on many vesicles as well as other membrane features such as pits and perhaps tubules.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AP1G1_MOUSE | P228921gyu 1gyv 1w63 2a7b 3zy7 4hmy 4p6z

(-) Related Entries Specified in the PDB File

1gyu GAMMA-ADAPTIN APPENDAGE DOMAIN FROM CLATHRIN ADAPTOR AP1
1gyv GAMMA-ADAPTIN APPENDAGE DOMAIN FROM CLATHRIN ADAPTOR AP1, L762E MUTANT