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(-) Description

Title :  X-RAY STRUCTURE OF HUMAN TPC6
 
Authors :  D. Kummel, J. J. Mueller, Y. Roske, R. Misselwitz, K. Bussow, U. Heinem
Date :  04 Feb 05  (Deposition) - 20 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tpc6, Trapp Complex, Tethering, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kummel, J. J. Mueller, Y. Roske, R. Misselwitz, K. Bussow, U. Heinemann
The Structure Of The Trapp Subunit Tpc6 Suggests A Model For A Trapp Subcomplex.
Embo Rep. V. 6 787 2005
PubMed-ID: 16025134  |  Reference-DOI: 10.1038/SJ.EMBOR.7400463

(-) Compounds

Molecule 1 - TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQTEV
    Expression System Strain: SCS1 ROSETTA
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: RZPD, GERMAN RESOURCE CENTRE
    Synonym: TPC6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:33 , LYS A:37 , ASN A:40 , ARG A:44 , HOH A:2055 , HOH A:2056 , HOH A:2057 , GLN B:47BINDING SITE FOR RESIDUE SO4 A1160
2AC2SOFTWARETYR A:21 , GLU A:28 , VAL A:29 , ASN A:31 , GLY A:32 , ARG A:33 , CYS A:34 , ILE A:35 , GOL A:1163BINDING SITE FOR RESIDUE SO4 A1161
3AC3SOFTWAREASN B:89 , GLN B:91 , ILE B:93 , MET B:156 , ILE B:157BINDING SITE FOR RESIDUE SO4 B1160
4AC4SOFTWAREGLY A:1 , PHE B:53 , THR B:54 , ARG B:59 , HOH B:2065 , HOH B:2066BINDING SITE FOR RESIDUE SO4 B1161
5AC5SOFTWAREGLN A:47 , ARG B:33 , LYS B:37 , ASN B:40 , ARG B:44 , HOH B:2067 , HOH B:2068BINDING SITE FOR RESIDUE SO4 B1162
6AC6SOFTWAREGLU A:39 , SER A:118 , ALA A:122 , THR A:142 , ALA A:143 , HOH A:2058 , LYS B:138BINDING SITE FOR RESIDUE GOL A1162
7AC7SOFTWARETYR A:21 , ILE A:35 , GLU A:115 , SO4 A:1161BINDING SITE FOR RESIDUE GOL A1163
8AC8SOFTWARELYS B:68 , CYS B:71 , LYS B:72 , ILE B:83BINDING SITE FOR RESIDUE GOL B1163
9AC9SOFTWARELYS A:138 , GLU B:39 , SER B:118 , ALA B:122 , THR B:142 , ALA B:143BINDING SITE FOR RESIDUE GOL B1164

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:148 -Pro A:149
2Met B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003301491cENSE00001846910chr14:39639526-39639219308TPC6B_HUMAN1-27272A:3-29
B:3-29		27
27
1.2aENST000003301492aENSE00001298290chr14:39628754-3962868768TPC6B_HUMAN28-50232A:30-52
B:30-52		23
23
1.2cENST000003301492cENSE00001318696chr14:39627606-39627489118TPC6B_HUMAN50-89402A:52-91 (gaps)
B:52-91		40
40
1.3ENST000003301493ENSE00001334158chr14:39623498-3962341584TPC6B_HUMAN90-117282A:92-119 (gaps)
B:92-119 (gaps)		28
28
1.4ENST000003301494ENSE00001297356chr14:39621043-3962095094TPC6B_HUMAN118-149322A:120-151
B:120-151		32
32
1.5bENST000003301495bENSE00001869808chr14:39619585-396170162570TPC6B_HUMAN149-158102A:151-159
B:151-159		9
9

(-) 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:143
 aligned with TPC6B_HUMAN | Q86SZ2 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:159
                              1                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148         
          TPC6B_HUMAN     - --MADEALFLLLHNEMVSGVYKSAEQGEVENGRCITKLENMGFRVGQGLIERFTKDTARFKDELDIMKFICKDFWTTVFKKQIDNLRTNHQGIYVLQDNKFRLLTQMSAGKQYLEHASKYLAFTCGLIRGGLSNLGIKSIVTAEVSSMPACKFQVMIQK 157
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh...---------.hhhhhhhh.hhhhhhh.....eeeeee..eeeeee...hhh...-------...hhh.hhhhhhhhhhhhh....eeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.1c  PDB: A:3-29     Exon 1.2a  PDB: A:30-52---------------------------------------Exon 1.3 UniProt: 90-117    Exon 1.4  PDB: A:120-151        -------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.2c  PDB: A:52-91 (gaps)          -----------------------------------------------------------Exon 1.5b Transcript 1 (2)
                 2bjn A   1 GSMADEALFLLLHNEMVSGVYKSAEQGEVENGRCITKLENMGFRVGQGLIERF---------ELDIMKFICKDFWTTVFKKQIDNLRTNHQGIYVLQDNKFRLLTQM-------EHASKYLAFTCGLIRGGLSNLGIKSIVTAEVSSMPACKFQVMIQK 159
                                    10        20        30        40        50  |      -  |     70        80        90       100      |  -    |  120       130       140       150         
                                                                               53        63                                         107     115                                            


Chain B from PDB  Type:PROTEIN  Length:149
 aligned with TPC6B_HUMAN | Q86SZ2 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:159
                              1                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148         
          TPC6B_HUMAN     - --MADEALFLLLHNEMVSGVYKSAEQGEVENGRCITKLENMGFRVGQGLIERFTKDTARFKDELDIMKFICKDFWTTVFKKQIDNLRTNHQGIYVLQDNKFRLLTQMSAGKQYLEHASKYLAFTCGLIRGGLSNLGIKSIVTAEVSSMPACKFQVMIQK 157
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhh.....eeee....eeeeee...hhh.----------..hhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.1c  PDB: B:3-29     Exon 1.2a  PDB: B:30-52---------------------------------------Exon 1.3 UniProt: 90-117    Exon 1.4  PDB: B:120-151        -------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.2c  PDB: B:52-91 UniProt: 50-89  -----------------------------------------------------------Exon 1.5b Transcript 1 (2)
                 2bjn B   1 GSMADEALFLLLHNEMVSGVYKSAEQGEVENGRCITKLENMGFRVGQGLIERFTKDTARFKDELDIMKFICKDFWTTVFKKQIDNLRTNHQGIYVLQDNKFRLLT----------HASKYLAFTCGLIRGGLSNLGIKSIVTAEVSSMPACKFQVMIQK 159
                                    10        20        30        40        50        60        70        80        90       100    |    -     | 120       130       140       150         
                                                                                                                                  105        116
   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 2BJN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BJN)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TPC6B_HUMAN | Q86SZ2)
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:0048208    COPII vesicle coating    The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
    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: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).

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 Related Entries

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

UniProtKB/Swiss-Prot
        TPC6B_HUMAN | Q86SZ2: 2cfh 3kxc

(-) Related Entries Specified in the PDB File

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