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Title :   CRYSTAL STRUCTURE OF THE RAB GTPASE SEC4P, THE SEC2P GEF DOMAIN, AND PHOSPHATE COMPLEX

Authors :   Y. Sato, S. Fukai, R. Ishitani, O. Nureki

Date :   30 Mar 07 (Deposition) - 22 May 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Coiled Coil, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Sato, S. Fukai, R. Ishitani, O. Nureki
Crystal Structure Of The Sec4P{Middle Dot}Sec2P Complex In The Nucleotide Exchanging Intermediate State
Proc. Natl. Acad. Sci. Usa V. 104 8305 2007
PubMed-ID: 17488829 | Reference-DOI: 10.1073/PNAS.0701550104
(for further references see the PDB file header)

Molecule 1 - RAS-RELATED PROTEIN SEC4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	ROSETTA (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 19-187
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	SUPPRESSOR OF RHO3 PROTEIN 6, RAB GTPASE SEC4P

Molecule 2 - RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR SEC2
	Chains	:	B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	ROSETTA (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	GEF DOMAIN, RESIDUES 51-142
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	GDP-GTP EXCHANGE FACTOR SEC2

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:28 , SER A:29 , GLY A:30 , VAL A:31 , GLY A:32 , LYS A:33 , SER A:34 , HOH A:204 , HOH A:227	BINDING SITE FOR RESIDUE PO4 A 201
2	AC2	SOFTWARE	LYS B:56 , ASN B:60 , LYS B:63 , ARG C:120 , LYS C:123 , HOH C:212	BINDING SITE FOR RESIDUE PO4 C 202

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

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

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAB	PS51419	small GTPase Rab1 family profile.	SEC4_YEAST	16-215	1	A:19-187

Asymmetric/Biological Unit (2, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YFL005W	1	YFL005W.1	VI:130329-130976	648	SEC4_YEAST	1-215	215	1	A:17-187 (gaps)	174

2.1	YNL272C	1	YNL272C.1	XIV:129084-126805	2280	SEC2_YEAST	1-759	759	2	B:50-142 C:50-142	93 93

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:171
 aligned with SEC4_YEAST | P07560 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:174
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183    
           SEC4_YEAST    14 GKSYDSIMKILLIGDSGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVDINGKKVKLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKIDSN 187
               SCOP domains d   2eqba_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .---.eeeeeeeee....hhhhhhhhhh.............eeeeeeee......eeeeeeee.....hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --RAB  PDB: A:19-187 UniProt: 16-215                                                                                                                                           PROSITE
               Transcript 1 Exon 1.1  PDB: A:17-187 (gaps) UniProt: 1-215 [INCOMPLETE]                                                                                                                     Transcript 1
                 2eqb A  17 G---SSIMKILLIGDSGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVDINGKKVKLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKIDSN 187
                            |   |   23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183    
                           17  18

Chain B from PDB  Type:PROTEIN  Length:93
 aligned with SEC2_YEAST | P17065 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:93
                                    59        69        79        89        99       109       119       129       139   
           SEC2_YEAST    50 ENYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQLREKDT 142
               SCOP domains -d2eqbb1 B:51-142 Rab guanine nucleotide exchange factor Sec2                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: B:50-142 UniProt: 1-759 [INCOMPLETE]                                           Transcript 2
                 2eqb B  50 SNYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQLREKDT 142
                                    59        69        79        89        99       109       119       129       139

Chain C from PDB  Type:PROTEIN  Length:93
 aligned with SEC2_YEAST | P17065 from UniProtKB/Swiss-Prot  Length:759

    Alignment length:93
                                    59        69        79        89        99       109       119       129       139   
           SEC2_YEAST    50 ENYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQLREKDT 142
               SCOP domains d2eqbc_ C: Rab guanine nucleotide exchange factor Sec2                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: C:50-142 UniProt: 1-759 [INCOMPLETE]                                           Transcript 2
                 2eqb C  50 SNYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQLREKDT 142
                                    59        69        79        89        99       109       119       129       139

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 '\|'

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Chain B,C (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.

Asymmetric/Biological Unit
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	SEC4_YEAST \| P07560
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UniProtKB/Swiss-Prot
	SEC2_YEAST \| P17065	:	2e7s 2ocy 4zdw
	SEC4_YEAST \| P07560	:	1g16 1g17 2ocy 3cph 4z8y 4zdw

2e7s	CRYSTAL STRUCTURE OF THE YEAST SEC2P GEF DOMAIN
2ocy	COMPLEX OF THE GUANINE EXHANGE FACTOR SEC2P AND THE RAB GTPASE SEC4P

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

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