RGD Reference Report - Molecular anatomy of a trafficking organelle. - Rat Genome Database

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Molecular anatomy of a trafficking organelle.

Authors: Takamori, Shigeo  Holt, Matthew  Stenius, Katinka  Lemke, Edward A  Grønborg, Mads  Riedel, Dietmar  Urlaub, Henning  Schenck, Stephan  Brügger, Britta  Ringler, Philippe  Müller, Shirley A  Rammner, Burkhard  Gräter, Frauke  Hub, Jochen S  De Groot, Bert L  Mieskes, Gottfried  Moriyama, Yoshinori  Klingauf, Jürgen  Grubmüller, Helmut  Heuser, John  Wieland, Felix  Jahn, Reinhard 
Citation: Takamori S, etal., Cell. 2006 Nov 17;127(4):831-46.
RGD ID: 12050113
Pubmed: PMID:17110340   (View Abstract at PubMed)
DOI: DOI:10.1016/j.cell.2006.10.030   (Journal Full-text)

Membrane traffic in eukaryotic cells involves transport of vesicles that bud from a donor compartment and fuse with an acceptor compartment. Common principles of budding and fusion have emerged, and many of the proteins involved in these events are now known. However, a detailed picture of an entire trafficking organelle is not yet available. Using synaptic vesicles as a model, we have now determined the protein and lipid composition; measured vesicle size, density, and mass; calculated the average protein and lipid mass per vesicle; and determined the copy number of more than a dozen major constituents. A model has been constructed that integrates all quantitative data and includes structural models of abundant proteins. Synaptic vesicles are dominated by proteins, possess a surprising diversity of trafficking proteins, and, with the exception of the V-ATPase that is present in only one to two copies, contain numerous copies of proteins essential for membrane traffic and neurotransmitter uptake.



Gene Ontology Annotations    Click to see Annotation Detail View

Cellular Component

  
Object SymbolSpeciesTermQualifierEvidenceWithNotesSourceOriginal Reference(s)
Rph3aRatextrinsic component of synaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Rph3aRatextrinsic component of synaptic vesicle membrane is_active_inIEP PMID:17110340SynGO 
Rph3aRatextrinsic component of synaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Snap29Ratextrinsic component of synaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Snap29Ratextrinsic component of synaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Stx2Ratsynapse is_active_inIDA PMID:17110340SynGO 
Stx2Ratsynapse is_active_inIEP PMID:17110340SynGO 
Exoc4Ratsynaptic vesicle is_active_inEXP PMID:17110340SynGO 
Exoc4Ratsynaptic vesicle is_active_inIDA PMID:17110340SynGO 
Sec22bRatsynaptic vesicle is_active_inEXP PMID:17110340SynGO 
Sec22bRatsynaptic vesicle is_active_inIDA PMID:17110340SynGO 
Stxbp5Ratsynaptic vesicle is_active_inEXP PMID:17110340SynGO 
Stxbp5Ratsynaptic vesicle is_active_inIEP PMID:17110340SynGO 
Stxbp5Ratsynaptic vesicle is_active_inIDA PMID:17110340SynGO 
Vps33bRatsynaptic vesicle is_active_inEXP PMID:17110340SynGO 
Vps33bRatsynaptic vesicle is_active_inIDA PMID:17110340SynGO 
Lamp1Ratsynaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Lamp1Ratsynaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Rab3aRatsynaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Rab3aRatsynaptic vesicle membrane is_active_inIEP PMID:17110340SynGO 
Rab3aRatsynaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Rab3bRatsynaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Rab3bRatsynaptic vesicle membrane is_active_inIEP PMID:17110340SynGO 
Rab3bRatsynaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Stx12Ratsynaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Stx12Ratsynaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Stx16Ratsynaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Stx16Ratsynaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Stx6Ratsynaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Stx6Ratsynaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Stx7Ratsynaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Stx7Ratsynaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Syngr1Ratsynaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Syngr1Ratsynaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Sypl1Ratsynaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Sypl1Ratsynaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Vamp2Ratsynaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Vamp2Ratsynaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Vamp3Ratsynaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Vamp3Ratsynaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 
Vamp3Ratsynaptic vesicle membrane is_active_inIEP PMID:17110340SynGO 
Wfs1Ratsynaptic vesicle membrane is_active_inEXP PMID:17110340SynGO 
Wfs1Ratsynaptic vesicle membrane is_active_inIDA PMID:17110340SynGO 

Objects Annotated

Genes (Rattus norvegicus)
Exoc4  (exocyst complex component 4)
Lamp1  (lysosomal-associated membrane protein 1)
Rab3a  (RAB3A, member RAS oncogene family)
Rab3b  (RAB3B, member RAS oncogene family)
Rph3a  (rabphilin 3A)
Sec22b  (SEC22 homolog B, vesicle trafficking protein)
Snap29  (synaptosome associated protein 29)
Stx12  (syntaxin 12)
Stx16  (syntaxin 16)
Stx2  (syntaxin 2)
Stx6  (syntaxin 6)
Stx7  (syntaxin 7)
Stxbp5  (syntaxin binding protein 5)
Syngr1  (synaptogyrin 1)
Sypl1  (synaptophysin-like 1)
Vamp2  (vesicle-associated membrane protein 2)
Vamp3  (vesicle-associated membrane protein 3)
Vps33b  (VPS33B, late endosome and lysosome associated)
Wfs1  (wolframin ER transmembrane glycoprotein)

Objects referenced in this article
Gene Atp6v0a1 ATPase H+ transporting V0 subunit a1 Rattus norvegicus
Gene Atp6v1b1 ATPase H+ transporting V1 subunit B1 Rattus norvegicus
Gene Rab11b RAB11B, member RAS oncogene family Rattus norvegicus
Gene Rab5a RAB5A, member RAS oncogene family Rattus norvegicus
Gene Rab5al1 Rab5a, member RAS oncogene family-like 1 Rattus norvegicus
Gene Sv2a synaptic vesicle glycoprotein 2a Rattus norvegicus
Gene Syn1 synapsin I Rattus norvegicus
Gene Syt1 synaptotagmin 1 Rattus norvegicus
Gene Vamp7 vesicle-associated membrane protein 7 Rattus norvegicus

Additional Information