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(-) Description

Title :  CRYSTAL STRUCTURE OF SLY1P IN COMPLEX WITH AN N-TERMINAL PEPTIDE OF SED5P
 
Authors :  A. Bracher, W. Weissenhorn
Date :  17 Sep 02  (Deposition) - 20 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Sm-Protein, Snare, Syntaxin, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bracher, W. Weissenhorn
Structural Basis For The Golgi Membrane Recruitment Of Sly1P By Sed5P
Embo J. V. 21 6114 2002
PubMed-ID: 12426383  |  Reference-DOI: 10.1093/EMBOJ/CDF608
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SLY1 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-TEV
    Expression System Strain: BL21 CODON+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: SLY1P
 
Molecule 2 - INTEGRAL MEMBRANE PROTEIN SED5
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM30
    Expression System Strain: BL21 CODON+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: SED5P

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1MQS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SLY1_YEAST_001 *E532KSLY1_YEAST  ---  ---AE532K
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SLY1_YEAST_001 *E532KSLY1_YEAST  ---  ---AE532K
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SLY1_YEAST_001 *E532KSLY1_YEAST  ---  ---AE532K
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR189W1YDR189W.1IV:838390-8403902001SLY1_YEAST1-6666661A:10-662 (gaps)653
2.1YLR026C1YLR026C.1XII:196473-1954511023SED5_YEAST1-3403401B:1-2121

(-) Sequences/Alignments

Asymmetric 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:588
 aligned with SLY1_YEAST | P22213 from UniProtKB/Swiss-Prot  Length:666

    Alignment length:653
                                    19        29        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   
           SLY1_YEAST    10 KDISLRDMQISAILKMLFLNKDLNNNDNITTITDDIFNQQEIIWKVLILDIKSTATISSVLRVNDLLKAGITVHSLIKQDRSPLPDVPAIYFVSPTKENIDIIVNDLKSDKYSEFYINFTSSLPRNLLEDLAQQVSITGKSDKIKQVYDQYLDFIVTEPELFSLEISNAYLTLNDPKTTEEEITGLCANIADGLFNTVLTINSIPIIRAAKGGPAEIIAEKLGTKLRDFVINTNSSSTSTLQGNDSLERGVLIILDRNIDFASMFSHSWIYQCMVFDIFKLSRNTVTIPLESKENGTDNTTAKPLATKKYDIEPNDFFWMENSHLPFPEAAENVEAALNTYKEEAAEITRKTGVTNISDLDPNSNNDTVQIQEVVKKLPELTAKKNTIDTHMNIFAALLSQLESKSLDTFFEVEQDPGSTKTRSRFLDILKDGKTNNLEDKLRSFIVLYLTSTTGLPKDFVQNVENYFKENDYDINALKYVYKLREFMQLSNMSLQNKSLEDGSDSAFKPSNLTLSGIYGLTEGKLQGGVGSLISGIKKLLPEKKTIPITNVVDAIMDPLNSSQKNLETTDSYLYIDPKITRGSHTRKPKRQSYNKSLVFVVGGGNYLEYQNLQEWAHSQLHNPKKVMYGSTAITTPAEFLNEISRLGASNSS 662
               SCOP domains d1mqsa_ A: Sly1P protein                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------1mqsA01 A:19-158  [code=3.40.50.2060, no name defined]                                                                                      ----1mqsA02 A:163-276,A:557-662  [code=3.40.50.1910, no name defined]                                                 1mqsA03 A:277-413,A:52               9-549 Syntaxin Binding Protein 1; Chain A, domai                    n 2                             1mqsA04 A:414-509,A:550-556  [code=1.25.40.60, no name defined]                                                   -1mqsA03              1mqsA041mqsA02 A:163-276,A:557-662  [code=3.40.50.1910, no name defined]                                          CATH domains
               Pfam domains -------------------------------------------Sec1-1mqsA01 A:53-653                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    --------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..............hhhhhhhhh...eeeeehhhhhhhhh...hhhhhhhh.eeeeee.......eeeeeeeeee..hhhhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhh..hhh.eeeeee.....ee....eee....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhh...------------...eeeeee.hhhhhhhhh...hhhhhhhhhh......eee.---------------...eee.......hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh--------------------.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....------------------hhhhhhh.......hhhhhhhh......hhhhhhhhhhhh....hhhhhhhhh..eee...................eeeeeee...hhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:10-662 (gaps) UniProt: 1-666 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Transcript 1
                 1mqs A  10 KDISLRDmQISAILKmLFLNKDLNNNDNITTITDDIFNQQEIIWKVLILDIKSTATISSVLRVNDLLKAGITVHSLIKQDRSPLPDVPAIYFVSPTKENIDIIVNDLKSDKYSEFYINFTSSLPRNLLEDLAQQVSITGKSDKIKQVYDQYLDFIVTEPELFSLEISNAYLTLNDPKTTEEEITGLCANIADGLFNTVLTINSIPIIRAAKGGPAEIIAEKLGTKLRDFVINTNS------------ERGVLIILDRNIDFASmFSHSWIYQCmVFDIFKLSRNTVTIP---------------LATKKYDIEPNDFFWmENSHLPFPEAAENVEAALNTYKEEAAEITRKT--------------------EVVKKLPELTAKKNTIDTHmNIFAALLSQLESKSLDTFFEVEQDPGSTKTRSRFLDILKDGKTNNLEDKLRSFIVLYLTSTTGLPKDFVQNVENYFKENDYDINALKYVYKLREFmQLSNmSLQNKSL------------------YGLTEGKLQGGVGSLISGIKKLLPEKKTIPITNVVDAImDPLNSSQKNLETTDSYLYIDPKITRGSHTRKPKRQSYNKSLVFVVGGGNYLEYQNLQEWAHSQLHNPKKVmYGSTAITTPAEFLNEISRLGASNSS 662
                                   |19     |  29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239    |    -       259       269   |   279   |   289        |-         -    |  319       329       339       349       359 |       -         -  |    389       399 |     409       419       429       439       449       459       469       479       489       499  |    509         -       529       539       549       559      |569       579       589       599       609       619       629       639       649       659   
                                  17-MSE  25-MSE                                                                                                                                                                                                                    244          257             273-MSE   283-MSE        298             314            329-MSE                         361                  382                401-MSE                                                                                         497-MSE|    509                528                                   566-MSE                                                                637-MSE                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      502-MSE                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:26
 aligned with SED5_YEAST | Q01590 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:26
                                 1                    
                                 |   5        15      
           SED5_YEAST     - -----MNIKDRTSEFQQSVLSYKKRN  21
               SCOP domains -------------------------- SCOP domains
               CATH domains 1mqsB00 B:-4-21            CATH domains
               Pfam domains -----Sed5p-1mqsB01 B:1-21  Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
               Transcript 2 -----Exon 2.1  PDB: B:1-21 Transcript 2
                 1mqs B  -4 GAMAGMNIKDRTSEFQQSVLSYKKRN  21
                                     5        15
   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 Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (5, 5)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Sec1] (5)
(-)
Clan: no clan defined [family: Sed5p] (1)

(-) Gene Ontology  (26, 36)

Asymmetric Unit(hide GO term definitions)
Chain A   (SLY1_YEAST | P22213)
molecular function
    GO:0000149    SNARE binding    Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.
    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:0019905    syntaxin binding    Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse.
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:0035543    positive regulation of SNARE complex assembly    Any process that increases the frequency, rate or extent of assembly of the SNARE complex. The SNARE complex is a protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers.
    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:0046578    regulation of Ras protein signal transduction    Any process that modulates the frequency, rate or extent of Ras protein signal transduction.
    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:0006904    vesicle docking involved in exocytosis    The initial attachment of a vesicle membrane to a target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane, that contributes to exocytosis.
    GO:0048280    vesicle fusion with Golgi apparatus    The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi.
    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:0030134    COPII-coated ER to Golgi transport vesicle    A vesicle with a coat formed of the COPII coat complex proteins. The COPII coat complex is formed by the Sec23p/Sec24p and the Sec13p/Sec31p heterodimers. COPII-associated vesicles transport proteins from the rough endoplasmic reticulum to the Golgi apparatus (anterograde transport).
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0031201    SNARE complex    A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B   (SED5_YEAST | Q01590)
molecular function
    GO:0005484    SNAP receptor activity    Acting as a marker to identify a membrane and interacting selectively with one or more SNAREs on another membrane to mediate membrane fusion.
    GO:0000149    SNARE binding    Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.
    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:0006891    intra-Golgi vesicle-mediated transport    The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).
    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: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: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:0048278    vesicle docking    The initial attachment of a transport vesicle membrane to the target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane. Docking requires only that the two membranes come close enough for these proteins to interact and adhere.
    GO:0006906    vesicle fusion    Fusion of the membrane of a transport vesicle with its target membrane.
    GO:0048280    vesicle fusion with Golgi apparatus    The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi.
    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:0031201    SNARE complex    A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25.
    GO:0005801    cis-Golgi network    The network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts the endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SED5_YEAST | Q01590: 1pd0

(-) Related Entries Specified in the PDB File

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