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(-) Description

Title :  COMPLEX OF THE GUANINE EXCHANGE FACTOR SEC2P AND THE RAB GTPASE SEC4P
 
Authors :  K. M. Reinisch, G. Dong
Date :  21 Dec 06  (Deposition) - 27 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Rab, Gef, Guanine Exchange Factor, Coiled-Coil, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Dong, M. Medkova, P. Novick, K. M. Reinisch
A Catalytic Coiled Coil: Structural Insights Into The Activation Of The Rab Gtpase Sec4P By Sec2P.
Mol. Cell V. 25 455 2007
PubMed-ID: 17289591  |  Reference-DOI: 10.1016/J.MOLCEL.2007.01.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR SEC2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 17-167
    GeneSEC2
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymGDP-GTP EXCHANGE FACTOR SEC2
 
Molecule 2 - RAS-RELATED PROTEIN SEC4
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 18-187
    GeneSEC4, SRO6
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymSUPPRESSOR OF RHO3 PROTEIN 6

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)ABC
Biological Unit 2 (2x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2OCY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (2, 3)

Asymmetric Unit (2, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YFL005W1YFL005W.1VI:130329-130976648SEC4_YEAST1-2152151C:18-186 (gaps)169

2.1YNL272C1YNL272C.1XIV:129084-1268052280SEC2_YEAST1-7597592A:14-162
B:14-162
149
149

(-) 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:149
 aligned with SEC2_YEAST | P17065 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:149
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153         
           SEC2_YEAST    14 VTSLSTQLIESVDKQSHLEEQLNKSLKTIASQKAAIENYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQLREKDTLLDTLTLQLKNLKKVMHSLD 162
               SCOP domains --d2ocya1 A:16-162 Rab guanine nucleotide exchange factor Sec2                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:14-162 UniProt: 1-759 [INCOMPLETE]                                                                                                   Transcript 2
                 2ocy A  14 SmALSTQLIESVDKQSHLEEQLNKSLKTIASQKAAIENYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNmVADARKEKYAIEILNKRLTEQLREKDTLLDTLTLQLKNLKKVmHSLD 162
                             |      23        33        43        53        63        73        83        93       103       113 |     123       133       143       153    |    
                             |                                                                                                 115-MSE                                    158-MSE
                            15-MSE                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with SEC2_YEAST | P17065 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:149
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153         
           SEC2_YEAST    14 VTSLSTQLIESVDKQSHLEEQLNKSLKTIASQKAAIENYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQLREKDTLLDTLTLQLKNLKKVMHSLD 162
               SCOP domains --d2ocyb1 B:16-162 Rab guanine nucleotide exchange factor Sec2                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------Sec2p-2ocyB01 B:78-162                                                                Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------Sec2p-2ocyB02 B:78-162                                                                Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: B:14-162 UniProt: 1-759 [INCOMPLETE]                                                                                                   Transcript 2
                 2ocy B  14 SmALSTQLIESVDKQSHLEEQLNKSLKTIASQKAAIENYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNmVADARKEKYAIEILNKRLTEQLREKDTLLDTLTLQLKNLKKVmHSLD 162
                             |      23        33        43        53        63        73        83        93       103       113 |     123       133       143       153    |    
                             |                                                                                                 115-MSE                                    158-MSE
                            15-MSE                                                                                                                                               

Chain C from PDB  Type:PROTEIN  Length:147
 aligned with SEC4_YEAST | P07560 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:169
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177         
           SEC4_YEAST    18 DSIMKILLIGDSGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVDINGKKVKLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKIDS 186
               SCOP domains d2ocyc1 C:18-186 Rab-related protein Sec4                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Ras-2ocyC01 C:22-182                                                                                                                                             ---- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhh.............eeeeee...------.eeeeee.....hhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhh......eeee.------------..hhhhhhh..........----...hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:18-186 (gaps) UniProt: 1-215 [INCOMPLETE]                                                                                                                Transcript 1
                 2ocy C  18 DSImKILLIGDSGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVD------KLQLWDTAGQERFRTITTAYYRGAmGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVG------------DQGEALAKELGIPFIESSA----NVNEIFFTLAKLIQEKIDS 186
                               |    27        37        47        57     |   -  |     77        87      | 97       107       117       127    |    -       147       157     |   -|      177         
                              21-MSE                                    63     70                      94-MSE                               132          145               163  168                  

   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  (2, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 3)

Asymmetric Unit

(-) Gene Ontology  (31, 37)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SEC2_YEAST | P17065)
molecular function
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0070273    phosphatidylinositol-4-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position.
biological process
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    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: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.
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:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0030133    transport vesicle    Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

Chain C   (SEC4_YEAST | P07560)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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:0031321    ascospore-type prospore assembly    During ascospore formation, the process in which each haploid nucleus becomes encapsulated by a double membrane.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    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:0007107    membrane addition at site of cytokinesis    Any process involved in the net addition of membrane at the site of cytokinesis; includes vesicle recruitment and fusion, local lipid synthesis and insertion.
    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:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    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:0006906    vesicle fusion    Fusion of the membrane of a transport vesicle with its target membrane.
cellular component
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0000131    incipient cellular bud site    The portion of the budding yeast plasma membrane where a daughter cell will emerge. The yeast marks this spot with bud-site selection proteins before bud emergence occurs. Actin is polarized to this spot just prior to and during bud emergence.
    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.
    GO:0030133    transport vesicle    Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.
    GO:0030658    transport vesicle membrane    The lipid bilayer surrounding a transport vesicle.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SEC2_YEAST | P170652e7s 2eqb 4zdw
        SEC4_YEAST | P075601g16 1g17 2eqb 3cph 4z8y 4zdw

(-) Related Entries Specified in the PDB File

1g16 SEC4P +GDP
1g17 SEC4P + GUANOSINE-5'-(BETA, GAMMA)-IMMIDOTRIPHOSPHATE