1G16 - JenaLib

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Title :   CRYSTAL STRUCTURE OF SEC4-GDP

Authors :   C. Stroupe, A. T. Brunger

Date :   10 Oct 00 (Deposition) - 11 Dec 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   G Protein Rab, Signaling Protein, Endocytosis/Exocytosis Complex, Signaling Protein, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Stroupe, A. T. Brunger
Crystal Structures Of A Rab Protein In Its Inactive And Active Conformations.
J. Mol. Biol. V. 304 585 2000
PubMed-ID: 11099382 | Reference-DOI: 10.1006/JMBI.2000.4236
(for further references see the PDB file header)

Molecule 1 - RAS-RELATED PROTEIN SEC4
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T-1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 18-187
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	GTP-BINDING PROTEIN SEC4

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 24)

No.	Name	Count	Type	Full Name
1	CO	8	Ligand/Ion	COBALT (II) ION
2	GDP	4	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:34 , GDP A:201 , HOH A:401 , HOH A:402 , HOH A:403 , HOH A:404	BINDING SITE FOR RESIDUE CO A 301
02	AC2	SOFTWARE	SER C:34 , GDP C:203 , HOH C:405 , HOH C:406 , HOH C:407 , HOH C:408	BINDING SITE FOR RESIDUE CO C 302
03	AC3	SOFTWARE	SER D:34 , GDP D:204 , HOH D:409 , HOH D:410 , HOH D:411 , HOH D:412	BINDING SITE FOR RESIDUE CO D 303
04	AC4	SOFTWARE	SER B:34 , GDP B:202 , HOH B:413 , HOH B:414 , HOH B:415 , HOH B:416	BINDING SITE FOR RESIDUE CO B 304
05	AC5	SOFTWARE	ASP A:43 , ASP A:166 , HOH A:418 , HOH A:419 , HIS C:121	BINDING SITE FOR RESIDUE CO A 305
06	AC6	SOFTWARE	HIS A:121 , ASP C:166 , ASN C:170 , HOH C:420 , HOH C:421 , HOH C:422 , HOH C:429	BINDING SITE FOR RESIDUE CO C 306
07	AC7	SOFTWARE	HIS B:121 , ASP D:43 , ASP D:166 , HOH D:423 , HOH D:424 , HOH D:425	BINDING SITE FOR RESIDUE CO D 307
08	AC8	SOFTWARE	ASP B:43 , ASP B:166 , HIS D:121 , HOH D:426 , HOH D:427	BINDING SITE FOR RESIDUE CO D 308
09	AC9	SOFTWARE	SER A:29 , GLY A:30 , VAL A:31 , GLY A:32 , LYS A:33 , SER A:34 , CYS A:35 , PHE A:45 , PRO A:47 , ASN A:133 , LYS A:134 , ASP A:136 , MSE A:137 , SER A:162 , ALA A:163 , LYS A:164 , CO A:301 , HOH A:401 , HOH A:403 , HOH A:404 , HOH A:450 , HOH A:522 , HOH A:626	BINDING SITE FOR RESIDUE GDP A 201
10	BC1	SOFTWARE	SER B:29 , GLY B:30 , VAL B:31 , GLY B:32 , LYS B:33 , SER B:34 , CYS B:35 , PHE B:45 , PRO B:47 , ASN B:133 , LYS B:134 , ASP B:136 , MSE B:137 , SER B:162 , ALA B:163 , LYS B:164 , CO B:304 , HOH B:413 , HOH B:415 , HOH B:416 , HOH B:678	BINDING SITE FOR RESIDUE GDP B 202
11	BC2	SOFTWARE	SER C:29 , GLY C:30 , VAL C:31 , GLY C:32 , LYS C:33 , SER C:34 , CYS C:35 , PHE C:45 , PRO C:47 , ASN C:133 , LYS C:134 , ASP C:136 , MSE C:137 , SER C:162 , ALA C:163 , LYS C:164 , CO C:302 , HOH C:405 , HOH C:406 , HOH C:408 , HOH C:579	BINDING SITE FOR RESIDUE GDP C 203
12	BC3	SOFTWARE	SER D:29 , GLY D:30 , VAL D:31 , GLY D:32 , LYS D:33 , SER D:34 , CYS D:35 , PHE D:45 , PRO D:47 , ASN D:133 , LYS D:134 , ASP D:136 , MSE D:137 , SER D:162 , ALA D:163 , LYS D:164 , CO D:303 , HOH D:409 , HOH D:411 , HOH D:412	BINDING SITE FOR RESIDUE GDP D 204

(no "SS Bond" information available for 1G16)

(no "Cis Peptide Bond" information available for 1G16)

(no "SAP(SNP)/Variant" information available for 1G16)

(no "PROSITE Motif" information available for 1G16)

Asymmetric/Biological Unit (1, 4)

	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	4	A:19-184 (gaps) B:19-186 (gaps) C:19-185 D:20-186 (gaps)	166 168 167 167

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
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Chain A from PDB  Type:PROTEIN  Length:159
 aligned with SEC4_YEAST | P07560 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:166
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178      
           SEC4_YEAST    19 SIMKILLIGDSGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVDINGKKVKLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKI 184
               SCOP domains d1g16a_ A: Rab-related protei       n Sec4                                                                                                                             SCOP domains
               CATH domains 1g16A00 A:19-184 P-loop conta       ining nucleotide triphosphate hydrolases                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh....-------..eeeeeee....eeeeeee...hhhhh...hhhhhh.eeeeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:19-184 (gaps) UniProt: 1-215 [INCOMPLETE]                                                                                                             Transcript 1
                 1g16 A  19 SImKILLIGDSGVGKSCLLVRFVEDKFNP-------IDFKIKTVDINGKKVKLQIWDTAGQERFRTITTAYYRGAmGIILVYDITDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDmETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKI 184
                              |     28        38        |-      | 58        68        78        88     |  98       108       118       128       138       148       158       168       178      
                              |                        47      55                                     94-MSE                                    137-MSE                                           
                             21-MSE

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with SEC4_YEAST | P07560 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:168
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178        
           SEC4_YEAST    19 SIMKILLIGDSGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVDINGKKVKLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKIDS 186
               SCOP domains d1g16b_ B: Rab-related protei       n Sec4                                                                                                                               SCOP domains
               CATH domains 1g16B00 B:19-186 P-loop conta       ining nucleotide triphosphate hydrolases                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh.....-------..eeeeeee....eeeeeeee..........hhhhhh.eeeeeeeee..hhhhhhhhhhhhhhhhh......eeeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:19-186 (gaps) UniProt: 1-215 [INCOMPLETE]                                                                                                               Transcript 1
                 1g16 B  19 SImKILLIGDSGVGKSCLLVRFVEDKFNP-------IDFKIKTVDINGKKVKLQIWDTAGQERFRTITTAYYRGAmGIILVYDITDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDmETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKIDS 186
                              |     28        38        |-      | 58        68        78        88     |  98       108       118       128       138       148       158       168       178        
                             21-MSE                    47      55                                     94-MSE                                    137-MSE

Chain C from PDB  Type:PROTEIN  Length:167
 aligned with SEC4_YEAST | P07560 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:167
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       
           SEC4_YEAST    19 SIMKILLIGDSGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVDINGKKVKLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKID 185
               SCOP domains d1g16c_ C: Rab-related protein Sec4                                                                                                                                     SCOP domains
               CATH domains 1g16C00 C:19-185 P-loop containing nucleotide triphosphate hydrolases                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh.............eeeeeee....eeeeeee..hhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:19-185 UniProt: 1-215 [INCOMPLETE]                                                                                                                     Transcript 1
                 1g16 C  19 SImKILLIGDSGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVDINGKKVKLQIWDTAGQERFRTITTAYYRGAmGIILVYDITDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDmETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKID 185
                              |     28        38        48        58        68        78        88     |  98       108       118       128       138       148       158       168       178       
                             21-MSE                                                                   94-MSE                                    137-MSE

Chain D from PDB  Type:PROTEIN  Length:160
 aligned with SEC4_YEAST | P07560 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:167
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       
           SEC4_YEAST    20 IMKILLIGDSGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVDINGKKVKLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKIDS 186
               SCOP domains d1g16d_ D: Rab-related prote       in Sec4                                                                                                                              SCOP domains
               CATH domains 1g16D00 D:20-186 P-loop cont       aining nucleotide triphosphate hydrolases                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh....-------..eeeeeeee..eeeeeeee..hhhhhhhh..........eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:20-186 (gaps) UniProt: 1-215 [INCOMPLETE]                                                                                                              Transcript 1
                 1g16 D  20 ImKILLIGDSGVGKSCLLVRFVEDKFNP-------IDFKIKTVDINGKKVKLQIWDTAGQERFRTITTAYYRGAmGIILVYDITDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDmETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKIDS 186
                             |      29        39       | -     |  59        69        79        89    |   99       109       119       129       139       149       159       169       179       
                            21-MSE                    47      55                                     94-MSE                                    137-MSE

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: G proteins (693)

Protein domain: Rab-related protein Sec4 (3)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

1a	d1g16a_	A:
1b	d1g16b_	B:
1c	d1g16c_	C:
1d	d1g16d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Baker's yeast (Saccharomyces cerevisiae) (61)

1a	1g16C00	C:19-185
1b	1g16B00	B:19-186
1c	1g16D00	D:20-186
1d	1g16A00	A:19-184

(no "Pfam Domain" information available for 1G16)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1g16)

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	1g16
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	SEC4_YEAST \| P07560	:	1g17 2eqb 2ocy 3cph 4z8y 4zdw

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 24)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (1, 4)

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