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(-) Description

Title :  CRYSTAL STRUCTURE ANALYS OF THE GAMMA-COPI APPENDAGE DOMAIN
 
Authors :  P. J. Watson, G. Frigerio, B. M. Collins, R. Duden, D. J. Owen
Date :  09 Oct 03  (Deposition) - 28 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Appendage; Beta Sandwich; Coatomer; Adp-Ribosylation Factors, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. J. Watson, G. Frigerio, B. M. Collins, R. Duden, D. J. Owen
Gamma-Cop Appendage Domain - Structure And Function
Traffic V. 5 79 2004
PubMed-ID: 14690497  |  Reference-DOI: 10.1111/J.1600-0854.2004.00158.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COATOMER GAMMA SUBUNIT
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGAMMA1-COP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:77 , HOH A:114 , HOH A:115 , HOH A:141 , HOH A:243 , ASP A:671BINDING SITE FOR RESIDUE MG A 875

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R4X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R4X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_054039M681TCOPG1_HUMANPolymorphism15648AM681T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R4X)

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003147971aENSE00002082831chr3:128968449-128968589141COPG1_HUMAN1-13130--
1.2aENST000003147972aENSE00001506810chr3:128969525-12896957753COPG1_HUMAN13-30180--
1.3ENST000003147973ENSE00001273101chr3:128971124-12897120481COPG1_HUMAN31-57270--
1.4aENST000003147974aENSE00001273091chr3:128971466-12897153772COPG1_HUMAN58-81240--
1.4dENST000003147974dENSE00001506809chr3:128971719-12897179880COPG1_HUMAN82-108270--
1.5bENST000003147975bENSE00001273076chr3:128973511-12897358676COPG1_HUMAN108-133260--
1.6cENST000003147976cENSE00001273070chr3:128973828-12897392093COPG1_HUMAN134-164310--
1.7ENST000003147977ENSE00001273062chr3:128974911-12897499787COPG1_HUMAN165-193290--
1.8ENST000003147978ENSE00001293983chr3:128976313-128976470158COPG1_HUMAN194-246530--
1.9ENST000003147979ENSE00001328400chr3:128976570-128976703134COPG1_HUMAN246-291460--
1.10bENST0000031479710bENSE00001305285chr3:128979176-12897924368COPG1_HUMAN291-313230--
1.11ENST0000031479711ENSE00001330234chr3:128979462-128979650189COPG1_HUMAN314-376630--
1.12aENST0000031479712aENSE00001273027chr3:128982747-12898284296COPG1_HUMAN377-408320--
1.13bENST0000031479713bENSE00001273019chr3:128984392-128984635244COPG1_HUMAN409-490820--
1.14aENST0000031479714aENSE00001273012chr3:128985867-12898594276COPG1_HUMAN490-515260--
1.15ENST0000031479715ENSE00001273003chr3:128986780-128986883104COPG1_HUMAN515-550360--
1.16ENST0000031479716ENSE00001272992chr3:128987338-128987463126COPG1_HUMAN550-592431A:600-6067
1.17ENST0000031479717ENSE00001272980chr3:128987775-12898784369COPG1_HUMAN592-615241A:606-615 (gaps)24
1.18ENST0000031479718ENSE00001272966chr3:128990610-128990752143COPG1_HUMAN615-662481A:615-66248
1.19aENST0000031479719aENSE00001272959chr3:128991087-128991258172COPG1_HUMAN663-720581A:663-72058
1.20aENST0000031479720aENSE00001305758chr3:128991650-12899174798COPG1_HUMAN720-752331A:720-75233
1.22aENST0000031479722aENSE00001324786chr3:128993681-128993819139COPG1_HUMAN753-799471A:753-79947
1.23ENST0000031479723ENSE00001303168chr3:128994037-12899413599COPG1_HUMAN799-832341A:799-83234
1.24cENST0000031479724cENSE00001324609chr3:128996137-128996614478COPG1_HUMAN832-874431A:832-87342

(-) 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:274
 aligned with COPG1_HUMAN | Q9Y678 from UniProtKB/Swiss-Prot  Length:874

    Alignment length:288
                                   595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865        
          COPG1_HUMAN   586 MAEQRTESTPITAVKQPEKVAATRQEIFQEQLAAVPEFRGLGPLFKSSPEPVALTESETEYVIRCTKHTFTNHMVFQFDCTNTLNDQTLENVTVQMEPTEAYEVLCYVPARSLPYNQPGTCYTLVALPKEDPTAVACTFSCMMKFTVKDCDPTTGETDDEGYEDEYVLEDLEVTVADHIQKVMKLNFEAAWDEVGDEFEKEETFTLSTIKTLEEAVGNIVKFLGMHPCERSDKVPDNKNTHTLLLAGVFRGGHDILVRSRLLLLDTVTMQVTARSLEELPVDIILASV 873
               SCOP domains d1r4xa1 A              :600-762 Coatomer gamma subunit C-terminal domain, first subdomain                                                                                        d1r4xa2 A:763-873 Coatomer gamma subunit, C-terminal subdomain                                                  SCOP domains
               CATH domains 1r4xA01 A              :600-759 Clathrin adaptor appendage domain; domain 1                                                                                                   1r4xA02 A:760-873  [code=3.30.310.30, no name defined]                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........h--------------hhhhhhhhhhhhhhhh......ee....ee.......eeeeeeeee...eeeeeeeeee....eeeeeeeeeeee....eeeeee.eeee.....eeeeeeee..........eeeeeeeeeeeee............eeeeee...eeehhhh.eee....hhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhh.ee............eeeeeeeeee...eeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.16   ----------------------Exon 1.18  PDB: A:615-662 UniProt: 615-662      Exon 1.19a  PDB: A:663-720 UniProt: 663-720               --------------------------------Exon 1.22a  PDB: A:753-799 UniProt: 753-799    --------------------------------Exon 1.24c  PDB: A:832-873 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ------Exon 1.17               --------------------------------------------------------------------------------------------------------Exon 1.20a  PDB: A:720-752       ----------------------------------------------Exon 1.23  PDB: A:799-832         ----------------------------------------- Transcript 1 (2)
                 1r4x A 600 MHHHHHHMT--------------RQEIFQEQLAAVPEFRGLGPLFKSSPEPVALTESETEYVIRCTKHTFTNHMVFQFDCTNTLNDQTLENVTVQMEPTEAYEVLcYVPARSLPYNQPGTCYTLVALPKEDPTAVACTFSCMMKFTVKDCDPTTGETDDEGYEDEYVLEDLEVTVADHIQKVMKLNFEAAWDEVGDEFEKEETFTLSTIKTLEEAVGNIVKFLGMHPCERSDKVPDNKNTHTLLLAGVFRGGHDILVRSRLLLLDTVTMQVTARSLEELPVDIILASV 873
                                    |-         -   |   615       625       635       645       655       665       675       685     | 695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865        
                                  608            609                                                                               691-CAS                                                                                                                                                                                  

   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 1R4X)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (COPG1_HUMAN | Q9Y678)
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:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0051683    establishment of Golgi localization    The directed movement of the Golgi to a specific location.
    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:0072384    organelle transport along microtubule    The directed movement of an organelle along a microtubule, mediated by motor proteins. This process begins with the attachment of an organelle to a microtubule, and ends when the organelle reaches its final destination.
    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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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: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.

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 Related Entries

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(-) Related Entries Specified in the PDB File

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