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(-) Description

Title :  STRUCTURAL BASIS FOR VESICLE TETHERING BY THE DSL1 COMPLEX
 
Authors :  Y. Ren, P. D. Jeffrey, F. M. Hughson
Date :  14 Oct 09  (Deposition) - 10 Nov 09  (Release) - 29 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  C,D
Keywords :  Intracellular Trafficking, Dsl1 Complex, Multisubunit Tethering Complex, Snare Proteins, Endoplasmic Reticulum, Er-Golgi Transport, Membrane, Protein Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Ren, C. K. Yip, A. Tripathi, D. Huie, P. D. Jeffrey, T. Walz, F. M. Hughson
A Structure-Based Mechanism For Vesicle Capture By The Multisubunit Tethering Complex Dsl1.
Cell(Cambridge, Mass. ) V. 139 1119 2009
PubMed-ID: 20005805  |  Reference-DOI: 10.1016/J.CELL.2009.11.002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DSL1
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 332-686
    GeneKLLA0C02695G
    Organism CommonYEAST
    Organism ScientificKLUYVEROMYCES LACTIS
    Organism Taxid28985
    SynonymKLLA0C02695P
 
Molecule 2 - PROTEIN TRANSPORT PROTEIN SEC39
    ChainsD
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneSEC39, DSL3, YLR440C
    Organism CommonBREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymDEPENDENT ON SLY1-20 PROTEIN 3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 20)

Asymmetric/Biological Unit (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3K8P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K8P)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly D:30 -Ser D:31

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K8P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K8P)

(-) Exons   (0, 0)

(no "Exon" information available for 3K8P)

(-) 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 C from PDB  Type:PROTEIN  Length:295
 aligned with Q6CUS2_KLULA | Q6CUS2 from UniProtKB/TrEMBL  Length:686

    Alignment length:352
                                   342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682  
         Q6CUS2_KLULA   333 NIYTTLKFESMMQQRVIQIRSIPEEEYHELVSVQFKTDGGKYEKGEKQDLELSEKKTENGKDTESWGWNENQDSDEHDGWDEELDIDVDNVPIQVSVFVQSAAKVFTEFEQGCDTIGRSKVESIYLYKFNLLQTAFFAMVSEKVNDWTQLYKDVRYLYTENPKLLQLMELNSRRLDLNLNLIKKTIYKLVNDQLQELKDNERTPDWDITISSLLPYLKKTALPTLYKLEDNTILVALIRYIVHDLVIDNILHWRVISEKSSENLSEFIMLLLSGLEIPRLNLIETYRHSREKLGILSKILTAHLKDILEMFYEGEFFLFETDEIVQWIILLFADTPTRRDCIDEIRRVREEA 684
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Dsl1_N-3k8pC02      -----------------------------------------------------------------------Dsl1_C-3k8pC01 C:424-684                                                                                                                                                                                                                                              Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhh..eeee.---------------------------------------------------------.eeeehhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k8p C 333 NIYTTLKFESmmQQRVIQIRSIPEEEYHELVSVQ---------------------------------------------------------PIQVSVFVQSAAKVFTEFEQGCDTIGRSKVESIYLYKFNLLQTAFFAmVSEKVNDWTQLYKDVRYLYTENPKLLQLmELNSRRLDLNLNLIKKTIYKLVNDQLQELKDNERTPDWDITISSLLPYLKKTALPTLYKLEDNTILVALIRYIVHDLVIDNILHWRVISEKSSENLSEFImLLLSGLEIPRLNLIETYRHSREKLGILSKILTAHLKDILEmFYEGEFFLFETDEIVQWIILLFADTPTRRDCIDEIRRVREEA 684
                                   342||     352       362   |     -         -         -         -         -         - |     432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682  
                                    343-MSE                366                                                       424                                            471-MSE                      500-MSE                                                                                              601-MSE                                  642-MSE                                      
                                     344-MSE                                                                                                                                                                                                                                                                                                                                                

Chain D from PDB  Type:PROTEIN  Length:594
 aligned with SEC39_YEAST | Q12745 from UniProtKB/Swiss-Prot  Length:709

    Alignment length:655
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679     
          SEC39_YEAST    30 GSQSKYLEILCVLWPELDDPKNLLFLRELEEEVQSPEGEETTDEDVIVELLESDSSLIPLIESDTTTRSNRYHELQEFISKKLNNKTLENFEEWLRERILICNEMIPETPLLYSVLWETAKSKVLSTKFIGWVEGVLKPLDHLNKRLHLIFKINEWEKMPDSELFKIIFDGVEDMQGYIGIADVIEDELAPTLSYGKKWETFITEFFNKQQFSLKSDTNYQLFIKLYYSLEKGVKDNSEASRKLQSNVVDILFHNSENLFNLSSLTHKLDELWSILSGFPDEITIEEQKTITALEMKQFMEFFIKCSTKFSFKEIFAITQEEESAQLAHFSSLCHEEFNKANEISSFLQAMYETVLDISKDDKIFTRISMDEKLYSILEILLQMNEFAYIEAIIERFDYSNNTQIYELLVKFFWHFFNNASNGLRKEPEMKKASQTLQIIQKHMSQRAGTNLTKLEVLLEISDKLSHYSINLNKSHNGARDTAFKPSNILEYRDCPLDIISNLLELNPRLYKDLPTTKSLLFGIYDSLSINREGQTGKVEVDLMVLHIDYALVNLDFGTAYELGKQVFEICQEAGQHMMKALGDEHWLTFYQMGKFVDPNWVDNEIPTEIIVLQMSILGRLLEVCPLEEVEIVTSQWSTLELELSARDLVKDKYA 684
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Sec39-3k8pD01 D:30-684                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh....hhhhhhhhhhhhhh.--------------------------------------hhhhhhhhhhhh......hhhhhhhhhhhhhhh........hhhhhhh......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.-----------hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..---.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....eeee...eeeehhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..............hhhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......---------..hhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k8p D  30 GSQSKYLEILCVLWPELDDPKNLLFLRELEEEV--------------------------------------YHELQEFISKKLNNKTLENFEEWLRERILICNEmIPETPLLYSVLWETAKSKVLSTKFIGWVEGVLKPLDHLNKRLHLIFKINEWEKmPDSELFKIIFD-----------ADVIEDELAPTLSYGKKWETFITEFFNKQQFSLKSDTNYQLFIKLYYSLEKGVK---EASRKLQSNVVDILFHNSENLFNLSSLTHKLDELWSILSGFPDEITIEEQKTITALEmKQFmEFFIKCSTKFSFKEIFAITQEEESAQLAHFSSLCHEEFNKANEISSFLQAmYETVLDISKDDKIFTRISmDEKLYSILEILLQmNEFAYIEAIIERFDYSNNTQIYELLVKFFWHFFNNASNGLRKEPEmKKASQTLQIIQKHmSQRAGTNLTKLEVLLEISDKLSHYSINLN---------AFKPSNILEYRDCPLDIISNLLELNPRLYKDLPTTKSLLFGIYDSLSINREGQTGKVEVDLmVLHIDYALVNLDFGTAYELGKQVFEICQEAGQHmmKALGDEHWLTFYQmGKFVDPNWVDNEIPTEIIVLQmSILGRLLEVCPLEEVEIVTSQWSTLELELSARDLVKDKYA 684
                                    39        49        59  |      -         -         -         - |     109       119       129    |  139       149       159       169       179       189       199         - |     219       229       239       249       259    |  269       279       289       299       309       319     | 329       339       349       359       369       379|      389       399       409   |   419       429       439       449       459       469   |   479       489       499  |      -  |    519       529       539       549       559       569   |   579       589       599       609       619  |    629       639    |  649       659       669       679     
                                                           62                                    101                              134-MSE                                               188-MSE    199         211                                                  264 268                                                      325-MSE                                                380-MSE            399-MSE       413-MSE                                       459-MSE       473-MSE                      502       512                                                          573-MSE                           607-MSE        622-MSE               644-MSE                                    
                                                                                                                                                                                                                                                                                                                                     329-MSE                                                                                                                                                                                                                                                                                608-MSE                                                                        

   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 3K8P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K8P)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit

(-) Gene Ontology  (14, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (Q6CUS2_KLULA | Q6CUS2)
biological process
    GO:0032581    ER-dependent peroxisome organization    A process of peroxisome organization in which assembly or arrangement of constituent parts takes place in the endoplasmic reticulum.
    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.
cellular component
    GO:0070939    Dsl1/NZR complex    A multisubunit tethering complex, i.e. a protein complex involved in mediating the initial interaction between vesicles and the membranes with which they fuse, that is involved in trafficking from the Golgi apparatus to the ER. In Saccharomyces cerevisiae the Dsl1p complex contains Dsl1p, Tip20p, and Sec39p.
    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).
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

Chain D   (SEC39_YEAST | Q12745)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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:0032581    ER-dependent peroxisome organization    A process of peroxisome organization in which assembly or arrangement of constituent parts takes place in the endoplasmic reticulum.
    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:0070939    Dsl1/NZR complex    A multisubunit tethering complex, i.e. a protein complex involved in mediating the initial interaction between vesicles and the membranes with which they fuse, that is involved in trafficking from the Golgi apparatus to the ER. In Saccharomyces cerevisiae the Dsl1p complex contains Dsl1p, Tip20p, and Sec39p.
    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).
    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:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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