Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF SRO7 FROM S. CEREVISIAE
 
Authors :  D. A. Hattendorf, W. I. Weis
Date :  15 Dec 06  (Deposition) - 03 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Wd40 Repeat, Beta Propeller, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. A. Hattendorf, A. Andreeva, A. Gangar, P. J. Brennwald, W. I. Weis
Structure Of The Yeast Polarity Protein Sro7 Reveals A Snare Regulatory Mechanism.
Nature V. 446 567 2007
PubMed-ID: 17392788  |  Reference-DOI: 10.1038/NATURE05635
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN SNI1
    ChainsA
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System Taxid4932
    GeneSNI1, SRO7
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymSUPPRESSOR OF RHO3 PROTEIN 7

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:835 , HIS A:851 , HOH A:1219 , HOH A:1220BINDING SITE FOR RESIDUE ZN A 963
2AC2SOFTWAREASP A:523 , SER A:525 , GLN A:530 , ASP A:531 , HOH A:1178 , HOH A:1203BINDING SITE FOR RESIDUE NA A 964

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Tyr A:441 -Pro A:442
2Arg A:461 -Pro A:462
3Gly A:665 -Pro A:666
4Gly A:741 -Pro A:742
5Ile A:841 -Pro A:842

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.SRO7_YEAST286-300  1A:286-300

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPR032W1YPR032W.1XVI:634120-6372213102SRO7_YEAST1-103310331A:62-951 (gaps)890

(-) 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:875
 aligned with SRO7_YEAST | Q12038 from UniProtKB/Swiss-Prot  Length:1033

    Alignment length:890
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951
           SRO7_YEAST    62 KNKIFSLAETNKYGMSSKPIAAAFDFTQNLLAIATVTGEVHIYGQQQVEVVIKLEDRSAIKEMRFVKGIYLVVINAKDTVYVLSLYSQKVLTTVFVPGKITSIDTDASLDWMLIGLQNGSMIVYDIDRDQLSSFKLDNLQKSSFFPAARLSPIVSIQWNPRDIGTVLISYEYVTLTYSLVENEIKQSFIYELPPFAPGGDFSEKTNEKRTPKVIQSLYHPNSLHIITIHEDNSLVFWDANSGHMIMARTVFETEINVPQPDYIRDSSTNAAKISKVYWMCENNPEYTSLLISHKSISRGDNQSLTMIDLGYTPRYSITSYEGMKNYYANPKQMKIFPLPTNVPIVNILPIPRQSPYFAGCHNPGLILLILGNGEIETMLYPSGIFTDKASLFPQNLSWLRPLATTSMAASVPNKLWLGALSAAQNKDYLLKGGVRTKRQKLPAEYGTAFITGHSNGSVRIYDASHGDIQDNASFEVNLSRTLNKAKELAVDKISFAAETLELAVSIETGDVVLFKYEVNQFYSVENRPESGDLEMNFRRFSLNNTNGVLVDVRDRAPTGVRQGFMPSTAVHANKGKTSAINNSNIGFVGIAYAAGSLMLIDRRGPAIIYMENIREISGAQSACVTCIEFVIMEYGDDGYSSILMVCGTDMGEVITYKILPASGGKFDVQLMDITNVTSKGPIHKIDAFSKETKSSCLATIPKMQNLSKGLCIPGIVLITGFDDIRLITLGKSKSTHKGFKYPLAATGLSYISTVEKNNDRKNLTVIITLEINGHLRVFTIPDFKEQMSEHIPFPIAAKYITESSVLRNGDIAIRVSEFQASLFSTVKEQDTLAPVSDTLYINGIRIPYRPQVNSLQWARGTVYCTPAQLNELLGGVNRPASKYKESIIAE 951
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Lgl_C-2oajA01 A:548-943                                                                                                                                                                                                                                                                                                                                                                                     -------- Pfam domains
         Sec.struct. author ....eeeeeeeeee....eeeeeee....eeeeee...eeeee.....eeeee......eeeeeee...eeeeee...eeeeee.....eeeeee....eeeee......eeeeee....eeeee....eeeeeee.hhhhhhh..........eeeee..eeeeeeee....eeeee....eeeeee........................eeeeee.....eeeeee....eeeee.....eeeee.......................eeeeeeeee.....eeeeeeeee.........eeeeeeee..hhhhhhhhhhhhhhhh..eeeee.......eeeeee.....hhhhhh....eeeeee....eeeee.....ee.hhhhhhhhhhhhh..eeeeeeeeeehhhhhhhhhh......................eeeeeeeee...eeeeee...........eeeehhhhh.......eeeeeee....eeeeee....eeeeeeee...---------------....hhhhh...eee.hhhh.....eeeeeeeee......eeeeee....eeeeee...eeeeee....eeeeeee.hhh.......eeeeeeeeee......eeeeeeeee...eeeeeeeee.hhh.eeeeeeeeee........eeeeee.........hhhhhhhhhhh....eeeeee...eeeee......eeeee....eeeeeeeeeeee.....eeeeeeeeeee...eeeeee.....eeeeee.....hhhhhh..ee.....eeee....eeeeeeee......................................hhhhhhhhhhh.......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD_REPEATS_1   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:62-951 (gaps) UniProt: 1-1033 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Transcript 1
                 2oaj A  62 KNKIFSLAETNKYGMSSKPIAAAFDFTQNLLAIATVTGEVHIYGQQQVEVVIKLEDRSAIKEMRFVKGIYLVVINAKDTVYVLSLYSQKVLTTVFVPGKITSIDTDASLDWMLIGLQNGSMIVYDIDRDQLSSFKLDNLQKSSFFPAARLSPIVSIQWNPRDIGTVLISYEYVTLTYSLVENEIKQSFIYELPPFAPGGDFSEKTNEKRTPKVIQSLYHPNSLHIITIHEDNSLVFWDANSGHMIMARTVFETEINVPQPDYIRDSSTNAAKISKVYWMCENNPEYTSLLISHKSISRGDNQSLTMIDLGYTPRYSITSYEGMKNYYANPKQMKIFPLPTNVPIVNILPIPRQSPYFAGCHNPGLILLILGNGEIETMLYPSGIFTDKASLFPQNLSWLRPLATTSMAASVPNKLWLGALSAAQNKDYLLKGGVRTKRQKLPAEYGTAFITGHSNGSVRIYDASHGDIQDNASFEVNLSRTLNKAKELAVDKISFAAETLELAVSIETGDVVLFKYEVNQF---------------FRRFSLNNTNGVLVDVRDRAPTGVRQGFMPSTAVHANKGKTSAINNSNIGFVGIAYAAGSLMLIDRRGPAIIYMENIREISGAQSACVTCIEFVIMEYGDDGYSSILMVCGTDMGEVITYKILPASGGKFDVQLMDITNVTSKGPIHKIDAFSKETKSSCLATIPKMQNLSKGLCIPGIVLITGFDDIRLITLGKSKSTHKGFKYPLAATGLSYISTVEKNNDRKNLTVIITLEINGHLRVFTIPDFKEQMSEHIPFPIAAKYITESSVLRNGDIAIRVSEFQASLFSTVKEQDTLAPVSDTLYINGIRIPYRPQVNSLQWARGTVYCTPAQLNELLGGVNRPASKYKESIIAE 951
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581|        -      |601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  582             598                                                                                                                                                                                                                                                                                                                                                                 

   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 2OAJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SRO7_YEAST | Q12038)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    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:0006893    Golgi to plasma membrane transport    The directed movement of substances from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane, where they fuse and release their contents by exocytosis.
    GO:0030010    establishment of cell polarity    The specification and formation of anisotropic intracellular organization or cell growth patterns.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0017157    regulation of exocytosis    Any process that modulates the frequency, rate or extent of exocytosis.
    GO:0050708    regulation of protein secretion    Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    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:0043332    mating projection tip    The apex of the mating projection in unicellular fungi exposed to mating pheromone; site of polarized growth.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:461 - Pro A:462   [ RasMol ]  
    Gly A:665 - Pro A:666   [ RasMol ]  
    Gly A:741 - Pro A:742   [ RasMol ]  
    Ile A:841 - Pro A:842   [ RasMol ]  
    Tyr A:441 - Pro A:442   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2oaj
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SRO7_YEAST | Q12038
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SRO7_YEAST | Q12038
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2OAJ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2OAJ)