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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE BET3-TRS31 HETERODIMER.
 
Authors :  Y. -G. Kim, B. -H. Oh
Date :  23 Aug 06  (Deposition) - 27 Nov 06  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Golgi Apparatus, Vesicle Transport, Er-Golgi Transport, Trapp, Palmitate, Transport, Lipoprotein, Endoplasmic Reticulum, Multisubunit Tethering Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. -G. Kim, S. Raunser, C. Munger, J. Wagner, Y. -L. Song, M. Cygler, T. Walz, B. -H. Oh, M. Sacher
The Architecture Of The Multisubunit Trapp I Complex Suggests A Model For Vesicle Tethering.
Cell(Cambridge, Mass. ) V. 127 817 2006
PubMed-ID: 17110339  |  Reference-DOI: 10.1016/J.CELL.2006.09.029

(-) Compounds

Molecule 1 - TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEXHTA, PET30A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: BET3 HOMOLOG
 
Molecule 2 - ZGC 92866
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEXHTA, PET30A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Common: ZEBRAFISH
    Organism Scientific: BRACHYDANIO RERIO
    Organism Taxid: 7955
    Synonym: TRS31

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NO31Ligand/IonNITRATE ION
2PLM1Ligand/IonPALMITIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:55 , CYS A:68 , LEU A:131 , ALA B:28BINDING SITE FOR RESIDUE PLM A1068
2AC2SOFTWAREPRO B:122 , LEU B:123 , ILE B:124 , LEU B:137 , ASN B:138 , CYS B:139 , ALA B:140BINDING SITE FOR RESIDUE NO3 B1177

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J3R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J3R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J3R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J3R)

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENSDART000000385741aENSDARE00000385444chr1:46134420-4613447253Q6DGL5_DANRE-00--
1.2ENSDART000000385742ENSDARE00000227628chr1:46134735-46135061327Q6DGL5_DANRE1-90901B:20-9071
1.3bENSDART000000385743bENSDARE00000227616chr1:46139301-46140137837Q6DGL5_DANRE91-188981B:91-17686

(-) 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:159
 aligned with TPPC3_MOUSE | O55013 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:163
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169   
          TPPC3_MOUSE    10 ESKKMSSELFTLTYGALVTQLCKDYENDEDVNKQLDRMGYNIGVRLIEDFLARSNVGRCHDFRETADVIAKVAFKMYLGITPSITNWSPAGDEFSLILENNPLVDFVELPDNHSALIYSNLLCGVLRGALEMVQMAVEAKFVQDTLKGDGVTEIRMRFIRRIE 172
               SCOP domains d2j3ra_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains 2j3rA00 A:10-172 Trafficking protein particle complex s   ubunit 3                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..---..hhhhhhhhhhhhhhhhhhh...eee.......eeeeee.....................hhhhhhhhhhhhhh.eeeeeee....-.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j3r A  10 ESKKMSSELFTLTYGALVTQLCKDYENDEDVNKQLDRMGYNIGVRLIEDFLARSN---CHDFRETADVIAKVAFKMYLGITPSITNWSPAGDEFSLILENNPLVDFVELPDNHSALIYSNLLCGVLRGALEMVQMAVEAKFVQDT-KGDGVTEIRMRFIRRIE 172
                                    19        29        39        49        59    |   69        79        89        99       109       119       129       139       149    | |159       169   
                                                                                 64  68                                                                                   154 |                
                                                                                                                                                                            156                


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with Q6DGL5_DANRE | Q6DGL5 from UniProtKB/TrEMBL  Length:188

    Alignment length:157
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       
         Q6DGL5_DANRE    20 PKTEVSVSAFALLFSEMVQYCQSRVYSVSELQARLADMGQGVGASLLDVLVMREKNGKRETKVLNILLFIKVNVWKALFGKEADKLEQANDDDKTYYIIEKEPLINAYISVPKENSTLNCAAFTGGIVEAILTHSGFPAKVTVHWHKGTTLMIKFDE 176
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....eeee......eeeeee..hhhhhhh........hhhhhhhhhhhhhhhhh....eeeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: B:20-90 UniProt: 1-90 [INCOMPLETE]                      Exon 1.3b  PDB: B:91-176 UniProt: 91-188 [INCOMPLETE]                                  Transcript 1
                 2j3r B  20 PKTEVSVSAFALLFSEMVQYCQSRVYSVSELQARLADMGQGVGASLLDVLVMREKNGKRETKVLNILLFIKVNVWKALFGKEADKLEQANDDDKTYYIIEKEPLINAYISVPKENSTLNCAAFTGGIVEAILTHSGFPAKVTVHWHKGTTLMIKFDE 176
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J3R)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TPPC3_MOUSE | O55013)
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).
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: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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0030008    TRAPP complex    A large complex that acts as a tethering factor involved in transporting vesicles from the ER through the Golgi to the plasma membrane. A TRAPP (transport protein particle) complex has a core set of proteins which are joined by specific subunits depending on the cellular component where a given TRAPP complex is active.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).

Chain B   (Q6DGL5_DANRE | Q6DGL5)
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TPPC3_MOUSE | O55013: 1wc8 1wc9 2j3t 2j3w 2pwn
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        Q6DGL5_DANRE | Q6DGL5: 2j3w

(-) Related Entries Specified in the PDB File

1vpg CRYSTAL STRUCTURE OF BET3 HOMOLOG (13277653) FROM MUSMUSCULUS AT 2.10 A RESOLUTION
1wc8 THE CRYSTAL STRUCTURE OF MOUSE BET3P
1wc9 THE CRYSTAL STRUCTURE OF TRUNCATED MOUSE BET3P.
2j3t THE CRYSTAL STRUCTURE OF THE BET3-TRS33- BET5-TRS23 COMPLEX.
2j3w THE CRYSTAL STRUCTURE OF THE BET3-TRS31- SEDLIN COMPLEX.