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(-) Description

Title :  CRYSTAL STRUCTURE OF COMPUTATIONALLY REDESIGNED GAMMA-ADAPTIN APPENDAGE DOMAIN FORMING A SYMMETRIC HOMODIMER
 
Authors :  P. B. Stranges, M. Machius, M. J. Miley, A. Tripathy, B. Kuhlman
Date :  17 Aug 11  (Deposition) - 28 Dec 11  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.09
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Keywords :  Endocytosis, Protein Design, Computational Design (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. B. Stranges, M. Machius, M. J. Miley, A. Tripathy, B. Kuhlman
Computational Design Of A Symmetric Homodimer Using Beta- Strand Assembly.
Proc. Natl. Acad. Sci. Usa V. 108 20562 2011
PubMed-ID: 22143762  |  Reference-DOI: 10.1073/PNAS.1115124108

(-) Compounds

Molecule 1 - AP-1 COMPLEX SUBUNIT GAMMA-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE-80L MBP FUSION VECTOR
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentCOMPUTATIONALLY REDESIGNED GAMMA-ADAPTIN APPENDAGE DOMAIN, RESIDUES 704-822
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymREDESIGNED CLATHRIN ADAPTOR AP1, ADAPTER-RELATED PROTEIN CO ADAPTOR PROTEIN COMPLEX AP-1 SUBUNIT GAMMA-1, CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 GAMMA-1 LARGE CHAIN, GAMMA-ADAPTIN, GAMMA1-ADAPTIN, GOLGI ADAPTOR HA1/AP1 ADAPTIN SUBUNIT GAMMA-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1IPA2Ligand/IonISOPROPYL ALCOHOL
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1IPA2Ligand/IonISOPROPYL ALCOHOL
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:8 , ALA A:10BINDING SITE FOR RESIDUE IPA A1121
2AC2SOFTWAREILE B:2 , SER B:4 , THR B:18 , PHE B:19 , GLU B:20 , HOH B:2027BINDING SITE FOR RESIDUE PEG B1121
3AC3SOFTWAREASP B:9 , ALA B:10 , GLY B:12 , LEU B:13 , LYS B:14 , SER B:36 , ASN B:37 , SER B:38 , ASN B:72BINDING SITE FOR RESIDUE PEG B1122
4AC4SOFTWARETYR B:8 , ALA B:10BINDING SITE FOR RESIDUE IPA B1123

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZY7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZY7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZY7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZY7)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZY7)

(-) 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:116
 aligned with AP1G1_MOUSE | P22892 from UniProtKB/Swiss-Prot  Length:822

    Alignment length:120
                                   712       722       732       742       752       762       772       782       792       802       812       822
          AP1G1_MOUSE   703 GIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ 822
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeee..----.eeeeeeeeee......eeeeeeee.....eeee........hhhhh..eeeeeeee........eeeeeeeee..eeeeeeeee...hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zy7 A   1 MIPSITAYDALGLKIEFTFERS----SVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTFNWNGYKVQSEAEVNNFPPQSWQ 120
                                    10        20 |    | 30        40        50        60        70        80        90       100       110       120
                                                22   27                                                                                             

Chain B from PDB  Type:PROTEIN  Length:116
 aligned with AP1G1_MOUSE | P22892 from UniProtKB/Swiss-Prot  Length:822

    Alignment length:120
                                   712       722       732       742       752       762       772       782       792       802       812       822
          AP1G1_MOUSE   703 GIPSITAYSKNGLKIEFTFERSNTNPSVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTYNHKGSAMQDLAEVNNFPPQSWQ 822
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeee..----.eeeeeeeeee......eeeeeeee.....eeee........hhhhh..eeeeeeee........eeeeeeeee..eeeeeeeee...hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zy7 B   1 MIPSITAYDALGLKIEFTFERS----SVTVITIQASNSTELDMTDFVFQAAVPKTFQLQLLSPSSSVVPAFNTGTITQVIKVLNPQKQQLRMRIKLTFNWNGYKVQSEAEVNNFPPQSWQ 120
                                    10        20 |    | 30        40        50        60        70        80        90       100       110       120
                                                22   27                                                                                             

   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 3ZY7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZY7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZY7)

(-) 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 1gyw 1w63 2a7b 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
1gyw GAMMA-ADAPTIN APPENDAGE DOMAIN FROM CLATHRIN ADAPTOR AP1 A753D MUTANT
1w63 AP1 CLATHRIN ADAPTOR CORE
2a7b ON THE ROUTINE USE OF SOFT X-RAYS IN MACROMOLECULAR CRYSTALLOGRAPHY, PART III- THE OPTIMAL DATA COLLECTION WAVELENGTH