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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE EXOCYST SUBUNIT SEC6P
 
Authors :  M. V. Sivaram, M. Munson
Date :  02 Jan 06  (Deposition) - 16 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  1,2
Biol. Unit 1:  1  (1x)
Biol. Unit 2:  2  (1x)
Keywords :  Exocyst Complex, Exocytosis, Tandem Helical Bundles, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. V. Sivaram, M. L. Furgason, D. N. Brewer, M. Munson
The Structure Of The Exocyst Subunit Sec6P Defines A Conserved Architecture With Diverse Roles.
Nat. Struct. Mol. Biol. V. 13 555 2006
PubMed-ID: 16699513  |  Reference-DOI: 10.1038/NSMB1096
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXOCYST COMPLEX COMPONENT SEC6
    Chains: 1, 2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3), BL21(DE3) RIL-X
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN SEC6CT2 (RESIDUES 411-805)
    Gene: SEC6
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2FJI)

(-) Sites  (0, 0)

(no "Site" information available for 2FJI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FJI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIL068C1YIL068C.1IX:235471-2330542418SEC6_YEAST1-80580521:407-805
2:407-805 (gaps)		399
399

(-) 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 1 from PDB  Type:PROTEIN  Length:399
 aligned with SEC6_YEAST | P32844 from UniProtKB/Swiss-Prot  Length:805

    Alignment length:399
                                   416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796         
           SEC6_YEAST   407 KSVIGDKEKETLFKDYLNLIVVKMTEWIGNLEKAEFDVFLERSTPPHSDSDGLLFLDGTKTCFQMFTQQVEVAAGTNQAKILVGVVERFSDLLTKRQKNWISKISEEIKKQINYNHKYDIDPESITPEDECPGGLVEYLIAVSNDQMKAADYAVAISSKYGKLVSKVYEKQITNHLEGTLDGFAEVAQCSSLGLITLMFDDLRKPYQEIFSKTWYMGSQAQQIADTLDEYLLDIKPQMNSVLFVNFIDNVIGETIIKFLTALSFEHSFKNKNNKFLEAMKRDFEIFYQLFVKVLDGNESKDTLITQNFTVMEFFMDLSCEPIDSILDIWQKYLEVYWDSRIDLLVGILKCRKDVSSSERKKIVQQATEMLHEYRRNMEANGVDREPTLMRRFVLEFEKQ 805
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.....eehhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: 1:407-805 UniProt: 1-805 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                            Transcript 1
                 2fji 1 407 GSHMGDKEKETLFKDYLNLIVVKMTEWIGNLEKAEFDVFLERSTPPHSDSDGLLFLDGTKTCFQMFTQQVEVAAGTNQAKILVGVVERFSDLLTKRQKNWISKISEEIKKQINYNHKYDIDPESITPEDECPGGLVEYLIAVSNDQMKAADYAVAISSKYGKLVSKVYEKQITNHLEGTLDGFAEVAQCSSLGLITLMFDDLRKPYQEIFSKTWYMGSQAQQIADTLDEYLLDIKPQMNSVLFVNFIDNVIGETIIKFLTALSFEHSFKNKNNKFLEAMKRDFEIFYQLFVKVLDGNESKDTLITQNFTVMEFFMDLSCEPIDSILDIWQKYLEVYWDSRIDLLVGILKCRKDVSSSERKKIVQQATEMLHEYRRNMEANGVDREPTLMRRFVLEFEKQ 805
                                   416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796         


Chain 2 from PDB  Type:PROTEIN  Length:396
 aligned with SEC6_YEAST | P32844 from UniProtKB/Swiss-Prot  Length:805

    Alignment length:399
                                   416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796         
           SEC6_YEAST   407 KSVIGDKEKETLFKDYLNLIVVKMTEWIGNLEKAEFDVFLERSTPPHSDSDGLLFLDGTKTCFQMFTQQVEVAAGTNQAKILVGVVERFSDLLTKRQKNWISKISEEIKKQINYNHKYDIDPESITPEDECPGGLVEYLIAVSNDQMKAADYAVAISSKYGKLVSKVYEKQITNHLEGTLDGFAEVAQCSSLGLITLMFDDLRKPYQEIFSKTWYMGSQAQQIADTLDEYLLDIKPQMNSVLFVNFIDNVIGETIIKFLTALSFEHSFKNKNNKFLEAMKRDFEIFYQLFVKVLDGNESKDTLITQNFTVMEFFMDLSCEPIDSILDIWQKYLEVYWDSRIDLLVGILKCRKDVSSSERKKIVQQATEMLHEYRRNMEANGVDREPTLMRRFVLEFEKQ 805
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.....eehhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....---....hhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: 2:407-805 (gaps) UniProt: 1-805 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 2fji 2 407 GSHMGDKEKETLFKDYLNLIVVKMTEWIGNLEKAEFDVFLERSTPPHSDSDGLLFLDGTKTCFQMFTQQVEVAAGTNQAKILVGVVERFSDLLTKRQKNWISKISEEIKKQINYNHKYDIDPESITPEDECPGGLVEYLIAVSNDQMKAADYAVAISSKYGKLVSKVYEKQITNHLEGTLDGFAEVAQCSSLGLITLMFDDLRKPYQEIFSKTWYMGSQAQQIADTLDEYLLDIKPQMNSVLFVNFIDNVIGETIIKFLTALSFEHSFKNKNNKFLEAMKRDFEIFYQLFVKVLDGNESKDTLITQNFTVMEFFMDLSCEPIDSILDIWQKYLEVYWDSRIDLLVGILKCRKDVSSSERKKIVQQATEMLHEYRRNMEA---DREPTLMRRFVLEFEKQ 805
                                   416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776        |-  |    796         
                                                                                                                                                                                                                                                                                                                                                                                                                    785 789
   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 2FJI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain 1,2   (SEC6_YEAST | P32844)
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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
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:0051601    exocyst localization    Any process in which an exocyst is transported to, or maintained in, a specific location. An exocyst is a protein complex peripherally associated with the plasma membrane that determines where vesicles dock and fuse.
    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:0035544    negative regulation of SNARE complex assembly    Any process that decreases 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: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:0090522    vesicle tethering involved in exocytosis    The initial, indirect interaction between a secretory vesicle membrane and a site of exocytosis in the plasma membrane. This interaction is mediated by tethering factors (or complexes), which interact with both membranes. Interaction can occur via direct binding to membrane phospholipids or membrane proteins, or via binding to vesicle coat proteins. This process is distinct from and prior to docking and fusion.
cellular component
    GO:0005935    cellular bud neck    The constriction between the mother cell and daughter cell (bud) in an organism that reproduces by budding.
    GO:0005934    cellular bud tip    The end of a cellular bud distal to the site of attachment to the mother cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000145    exocyst    A protein complex peripherally associated with the plasma membrane that determines where vesicles dock and fuse. At least eight complex components are conserved between yeast and mammals.

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