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Title :   CRYSTAL STRUCTURE OF YEAST RAB-GDI

Authors :   S. Kravchenko, A. Ignatev, R. S. Goody, A. Rak, O. Pylypenko

Date :   31 Mar 08 (Deposition) - 06 May 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : G,H
Biol. Unit 1: G  (1x)
Biol. Unit 2: H  (1x)

Keywords :   Rab, Gdi, Vesicular Transport, Cytoplasm, Gtpase Activation, Phosphoprotein, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Ignatev, S. Kravchenko, A. Rak, R. S. Goody, O. Pylypenko
A Structural Model Of The Gdp Dissociation Inhibitor Rab Membrane Extraction Mechanism.
J. Biol. Chem. V. 283 18377 2008
PubMed-ID: 18426803 | Reference-DOI: 10.1074/JBC.M709718200
(for further references see the PDB file header)

Molecule 1 - RAB GDP-DISSOCIATION INHIBITOR
	Chains	:	G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET19
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	RAB GDI, SECRETORY PATHWAY GDP DISSOCIATION INHIBITOR, YEAST RAB-GDI

		1	2
Asymmetric Unit	:	G	H
Biological Unit 1 (1x)	:	G
Biological Unit 2 (1x)	:		H

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3CPI)

(no "Site" information available for 3CPI)

(no "SS Bond" information available for 3CPI)

(no "Cis Peptide Bond" information available for 3CPI)

(no "SAP(SNP)/Variant" information available for 3CPI)

(no "PROSITE Motif" information available for 3CPI)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YER136W	1	YER136W.1	V:439612-440967	1356	GDI1_YEAST	1-451	451	2	G:7-443 H:5-443	437 439

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
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Chain G from PDB  Type:PROTEIN  Length:437
 aligned with GDI1_YEAST | P39958 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:437
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       
           GDI1_YEAST     7 DTDYDVIVLGTGITECILSGLLSVDGKKVLHIDKQDHYGGEAASVTLSQLYEKFKQNPISKEERESKFGKDRDWNVDLIPKFLMANGELTNILIHTDVTRYVDFKQVSGSYVFKQGKIYKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLDLDKNTMDEVYYKFGLGNSTKEFIGHAMALWTNDDYLQQPARPSFERILLYCQSVARYGKSPYLYPMYGLGELPQGFARLSAIYGGTYMLDTPIDEVLYKKDTGKFEGVKTKLGTFKAPLVIADPTYFPEKCKSTGQRVIRAICILNHPVPNTSNADSLQIIIPQSQLGRKSDIYVAIVSDAHNVCSKGHYLAIISTIIETDKPHIELEPAFKLLGPIEEKFMGIAELFEPREDGSKDNIYLSRSYDASSHFESMTDDVKDIYFRVTGHPLVLK 443
               SCOP domains d3cpig1 G:7-301 automated matches                                                                                                                                                                                                                                                                      d3cpig3 G:302-399 automated matches                                                               d3cpig2 G:400-443 automated matches          SCOP domains
               CATH domains 3cpiG01 G:7-61,G:232-305,G:398-443                     3cpiG02 G:62-126,G:306-397                                       3cpiG03 G:127-231 Guanine Nucleotide Dissociation Inhibitor, domain 1                                    3cpiG01 G:7-61,G:232-305,G:398-443  [code=3.50.50.60, no name defined]    3cpiG02 G:62-126,G:306-397 Guanine Nucleotide Dissociation Inhibitor, domain 2              3cpiG01 G:7-61,G:232-305,G:398-443             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhhh...eeee...........eehhhhhhhhhh....hhhhhhhhh.hhhhh.ee.....ee..hhhhhhhhhhhhhhh..eee..eeeeee..eeee...hhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhh.......hhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eee......eeee......eeeeee..eeee...eee.hhhhhh.eeeeeeeeeeeeeee............eeeeehhhhh.....eeeeeee.hhh......eeeeeeee....hhhhhhhhhhh......eeeeeeeeeeee........eee.........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: G:7-443 UniProt: 1-451 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                    Transcript 1
                 3cpi G   7 DTDYDVIVLGTGITECILSGLLSVDGKKVLHIDKQDHYGGEAASVTLSQLYEKFKQNPISKEERESKFGKDRDWNVDLIPKFLMANGELTNILIHTDVTRYVDFKQVSGSYVFKQGKIYKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLDLDKNTMDEVYYKFGLGNSTKEFIGHAMALWTNDDYLQQPARPSFERILLYCQSVARYGKSPYLYPMYGLGELPQGFARLSAIYGGTYMLDTPIDEVLYKKDTGKFEGVKTKLGTFKAPLVIADPTYFPEKCKSTGQRVIRAICILNHPVPNTSNADSLQIIIPQSQLGRKSDIYVAIVSDAHNVCSKGHYLAIISTIIETDKPHIELEPAFKLLGPIEEKFMGIAELFEPREDGSKDNIYLSRSYDASSHFESMTDDVKDIYFRVTGHPLVLK 443
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436

Chain H from PDB  Type:PROTEIN  Length:439
 aligned with GDI1_YEAST | P39958 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:439
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434         
           GDI1_YEAST     5 TIDTDYDVIVLGTGITECILSGLLSVDGKKVLHIDKQDHYGGEAASVTLSQLYEKFKQNPISKEERESKFGKDRDWNVDLIPKFLMANGELTNILIHTDVTRYVDFKQVSGSYVFKQGKIYKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLDLDKNTMDEVYYKFGLGNSTKEFIGHAMALWTNDDYLQQPARPSFERILLYCQSVARYGKSPYLYPMYGLGELPQGFARLSAIYGGTYMLDTPIDEVLYKKDTGKFEGVKTKLGTFKAPLVIADPTYFPEKCKSTGQRVIRAICILNHPVPNTSNADSLQIIIPQSQLGRKSDIYVAIVSDAHNVCSKGHYLAIISTIIETDKPHIELEPAFKLLGPIEEKFMGIAELFEPREDGSKDNIYLSRSYDASSHFESMTDDVKDIYFRVTGHPLVLK 443
               SCOP domains d3cpih1 H:5-301 automated matches                                                                                                                                                                                                                                                                        d3cpih3 H:302-399 automated matches                                                               d3cpih2 H:400-443 automated matches          SCOP domains
               CATH domains 3cpiH01 H:5-61,H:232-305,H:398-443                       3cpiH02 H:62-126,H:306-397                                       3cpiH03 H:127-231 Guanine Nucleotide Dissociation Inhibitor, domain 1                                    3cpiH01 H:5-61,H:232-305,H:398-443  [code=3.50.50.60, no name defined]    3cpiH02 H:62-126,H:306-397 Guanine Nucleotide Dissociation Inhibitor, domain 2              3cpiH01 H:5-61,H:232-305,H:398-443             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..hhhhhhhhhhhhhh...eeee...........eehhhhhhhhhh....hhhhhhhhh.hhhhh.ee.....ee..hhhhhhhhhhhhhhh..eee..eeeeee..eeee...hhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhh.......hhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eee......eeee......eeeeee..eeee..eeee.hhhhhh.eeeeeeeeeeeeeee............eeeeehhhhh.....eeeeeee.hhh......eeeeeeee....hhhhhhhhhhhh.....eeeeeeeeeeee........eee.........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: H:5-443 UniProt: 1-451 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                      Transcript 1
                 3cpi H   5 TIDTDYDVIVLGTGITECILSGLLSVDGKKVLHIDKQDHYGGEAASVTLSQLYEKFKQNPISKEERESKFGKDRDWNVDLIPKFLMANGELTNILIHTDVTRYVDFKQVSGSYVFKQGKIYKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLDLDKNTMDEVYYKFGLGNSTKEFIGHAMALWTNDDYLQQPARPSFERILLYCQSVARYGKSPYLYPMYGLGELPQGFARLSAIYGGTYMLDTPIDEVLYKKDTGKFEGVKTKLGTFKAPLVIADPTYFPEKCKSTGQRVIRAICILNHPVPNTSNADSLQIIIPQSQLGRKSDIYVAIVSDAHNVCSKGHYLAIISTIIETDKPHIELEPAFKLLGPIEEKFMGIAELFEPREDGSKDNIYLSRSYDASSHFESMTDDVKDIYFRVTGHPLVLK 443
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434

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 "Pfam Domain" information available for 3CPI)

Asymmetric Unit(hide GO term definitions)

Chain G,H (GDI1_YEAST | P39958)

molecular function
	GO:0005092	GDP-dissociation inhibitor activity	Prevents the dissociation of GDP from a GTPase, thereby preventing GTP from binding.
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0005093	Rab GDP-dissociation inhibitor activity	Prevents the dissociation of GDP from the small GTPase Rab, thereby preventing GTP from binding.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	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:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
	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: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:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	GDI1_YEAST \| P39958	:	1ukv 2bcg 3cph 3cpj

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