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(-) Description

Title :  STRUCTURAL IDENTIFICATION OF A CONSERVED APPENDAGE DOMAIN IN THE CARBOXYL-TERMINUS OF THE COPI GAMMA-SUBUNIT.
 
Authors :  G. R. Hoffman, P. B. Rahl, R. N. Collins, R. A. Cerione
Date :  10 Jul 03  (Deposition) - 14 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A
Keywords :  Platform Domain, Appendage Domain, Ear Domain, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. R. Hoffman, P. B. Rahl, R. N. Collins, R. A. Cerione
Conserved Structural Motifs In Intracellular Trafficking Pathways. Structure Of The Gammacop Appendage Domain.
Mol. Cell V. 12 615 2003
PubMed-ID: 14527408  |  Reference-DOI: 10.1016/J.MOLCEL.2003.08.002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COATOMER GAMMA SUBUNIT
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-KG
    Expression System StrainJM109
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 555-874
    GeneCOPG
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymGAMMA-COAT PROTEIN, GAMMA-COP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:99 , HOH A:139 , THR A:827 , ARG A:845BINDING SITE FOR RESIDUE SO4 A 350
2AC2SOFTWAREHOH A:73 , HOH A:152 , LEU A:626 , GLY A:627 , PHE A:655 , THR A:656 , ASP A:657 , HIS A:658BINDING SITE FOR RESIDUE SO4 A 351
3AC3SOFTWAREHOH A:31 , ASN A:676 , ARG A:843 , ARG A:845BINDING SITE FOR RESIDUE SO4 A 352

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PZD)

(-) Exons   (0, 0)

(no "Exon" information available for 1PZD)

(-) 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:271
 aligned with COPG1_BOVIN | P53620 from UniProtKB/Swiss-Prot  Length:874

    Alignment length:271
                                   613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873 
          COPG1_BOVIN   604 KVAATRQEIFQEQLAAVPEFQGLGPLFKSSPEPVALTESETEYVIRCTKHTFTDHMVFQFDCTNTLNDQTLENVTVQMEPSEAYEVLCYVPARSLPYNQPGTCYTLVALPKEDPTAVACTFSCVMKFTVKDCDPTTGEADDEGYEDEYVLEDLEVTIADHIQKVMKLNFEAAWDEVGDEFQKEETFTLSTIKTLEEAVGNIVKFLGMHPCERSDKVPDNKNTHTLLLAGVFRGGHDILVRSRLLLLDTVTMQVTARSSEELPVDIVLASVG 874
               SCOP domains d1pzda1 A:604-762 Coatomer gamma subunit C-terminal domain, first subdomain                                                                                    d1pzda2 A:763-874 Coatomer gamma subunit, C-terminal subdomain                                                   SCOP domains
               CATH domains 1pzdA01 A:604-759 Clathrin adaptor appendage domain; domain 1                                                                                               1pzdA02 A:760-874  [code=3.30.310.30, no name defined]                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh......ee....ee.......eeeeeeeee...eeeeeeeeee....eeeeeeeeeeee....eeeeee.eeee.....eeeeeeee..........eeeeeeeeeeeee............eeeeee...eeehhhh.eee....hhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhh.ee............eeeeeeeeee....eeeeeeeeee...eeeeeeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pzd A 604 KVAATRQEIFQEQLAAVPEFQGLGPLFKSSPEPVALTESETEYVIRCTKHTFTDHMVFQFDCTNTLNDQTLENVTVQMEPSEAYEVLCYVPARSLPYNQPGTCYTLVALPKEDPTAVACTFSCVMKFTVKDCDPTTGEADDEGYEDEYVLEDLEVTIADHIQKVMKLNFEAAWDEVGDEFQKEETFTLSTIKTLEEAVGNIVKFLGMHPCERSDKVPDNKNTHTLLLAGVFRGGHDILVRSRLLLLDTVTMQVTARSSEELPVDIVLASVG 874
                                   613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873 

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (COPG1_BOVIN | P53620)
molecular function
    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:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0006891    intra-Golgi vesicle-mediated transport    The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).
    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: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:0006890    retrograde vesicle-mediated transport, Golgi to ER    The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
    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:0030126    COPI vesicle coat    One of two multimeric complexes that forms a membrane vesicle coat. The mammalian COPI subunits are called alpha-, beta-, beta'-, gamma-, delta-, epsilon- and zeta-COP. Vesicles with COPI coats are found associated with Golgi membranes at steady state.
    GO:0030663    COPI-coated vesicle membrane    The lipid bilayer surrounding a COPI-coated vesicle.
    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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        COPG1_BOVIN | P536203tjz

(-) Related Entries Specified in the PDB File

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