2EFC - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ARA7-GDP/ATVPS9A

Authors :   T. Uejima, K. Ihara, T. Goh, E. Ito, M. Sunada, T. Ueda, A. Nakano, S. Waka

Date :   22 Feb 07 (Deposition) - 26 Feb 08 (Release) - 21 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Gef, Gtpase, Vps9, Rab5, Nucleotide, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Uejima, K. Ihara, T. Goh, E. Ito, M. Sunada, T. Ueda, A. Nakano, S. Wakatsuki
Gdp-Bound And Nucleotide-Free Intermediates Of The Guanine Nucleotide Exchange In The Rab5/Vps9 System
J. Biol. Chem. V. 285 36689 2010
PubMed-ID: 20833725 | Reference-DOI: 10.1074/JBC.M110.152132

Molecule 1 - SIMILARITY TO VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS9
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX4T1
	Expression System Strain	:	ROSETTA-GAMI(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	VPS9 DOMAIN
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	ATVPS9A, HYPOTHETICAL PROTEIN AT3G19770

Molecule 2 - SMALL GTP-BINDING PROTEIN-LIKE
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX4T1
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	GTPASE DOMAIN
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	ARA7, AT4G19640/F24J7_190

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:180 , ASP A:185 , HOH A:323 , ASP B:18 , GLY B:20 , ALA B:21 , GLY B:22 , LYS B:23 , SER B:24 , SER B:25 , ASN B:123 , LYS B:124 , ASP B:126 , SER B:153 , ALA B:154 , LYS B:155 , HOH B:1204 , HOH B:1208 , HOH B:1232	BINDING SITE FOR RESIDUE GDP B 1200
2	AC2	SOFTWARE	ASN C:180 , ASP C:185 , HOH C:280 , ASP D:18 , GLY D:20 , ALA D:21 , GLY D:22 , LYS D:23 , SER D:24 , SER D:25 , ASN D:123 , LYS D:124 , ASP D:126 , LEU D:127 , SER D:153 , ALA D:154 , LYS D:155 , HOH D:2208 , HOH D:2246	BINDING SITE FOR RESIDUE GDP D 2200

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

Asymmetric Unit

No.	Residues
1	Ser A:68	-	Gly A:69
2	Ser C:68	-	Gly C:69

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VPS9	PS51205	VPS9 domain profile.	VPS9A_ARATH	102-246	2	A:102-246 C:102-246

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VPS9	PS51205	VPS9 domain profile.	VPS9A_ARATH	102-246	1	A:102-246 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VPS9	PS51205	VPS9 domain profile.	VPS9A_ARATH	102-246	1	- C:102-246

(no "Exon" information available for 2EFC)

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:246
 aligned with VPS9A_ARATH | Q9LT31 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:246
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256      
          VPS9A_ARATH    17 MRKPSAGDFVKSIKSFIVSFSNNAPDPEKDCAMVQEFFSKMEAAFRAHPLWSGCSEEELDSAGDGLEKYVMTKLFTRVFASNTEEVIADEKLFQKMSLVQQFISPENLDIQPTFQNESSWLLAQKELQKINMYKAPRDKLVCILNCCKVINNLLLNASIASNENAPGADEFLPVLIYVTIKANPPQLHSNLLYIQRYRRESKLVGEAAYFFTNILSAESFISNIDAKSISLDEAEFEKNMESARAR 262
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------VPS9  PDB: A:102-246 UniProt: 102-246                                                                                                            ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2efc A  17 MRKPSAGDFVKSIKSFIVSFSNNAPDPEKDCAMVQEFFSKMEAAFRAHPLWSGCSEEELDSAGDGLEKYVMTKLFTRVFASNTEEVIADEKLFQKMSLVQQFISPENLDIQPTFQNESSWLLAQKELQKINMYKAPRDKLVCILNCCKVINNLLLNASIASNENAPGADEFLPVLIYVTIKANPPQLHSNLLYIQRYRRESKLVGEAAYFFTNILSAESFISNIDAKSISLDEAEFEKNMESARAR 262
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256

Chain B from PDB  Type:PROTEIN  Length:165
 aligned with RAF2B_ARATH | Q9SN68 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:165
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167     
          RAF2B_ARATH     8 SINAKLVLLGDVGAGKSSLVLRFVKDQFVEFQESTIGAAFFSQTLAVNDATVKFEIWDTAGQERYHSLAPMYYRGAAAAIIVFDVTNQASFERAKKWVQELQAQGNPNMVMALAGNKSDLLDARKVTAEDAQTYAQENGLFFMETSAKTATNVKEIFYEIARRLP 172
               SCOP domains d2efcb_ B: automated matches                                                                                                                                          SCOP domains
               CATH domains 2efcB00 B:8-172 P-loop containing nucleotide triphosphate hydrolases                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh.............eeeeee......eeeeeee...hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhh..eeee.......hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2efc B   8 SINAKLVLLGDVGAGKSSLVLRFVKDQFVEFQESTIGAAFFSQTLAVNDATVKFEIWDTAGQERYHSLAPMYYRGAAAAIIVFDVTNQASFERAKKWVQELQAQGNPNMVMALAGNKSDLLDARKVTAEDAQTYAQENGLFFMETSAKTATNVKEIFYEIARRLP 172
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167

Chain C from PDB  Type:PROTEIN  Length:246
 aligned with VPS9A_ARATH | Q9LT31 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:246
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256      
          VPS9A_ARATH    17 MRKPSAGDFVKSIKSFIVSFSNNAPDPEKDCAMVQEFFSKMEAAFRAHPLWSGCSEEELDSAGDGLEKYVMTKLFTRVFASNTEEVIADEKLFQKMSLVQQFISPENLDIQPTFQNESSWLLAQKELQKINMYKAPRDKLVCILNCCKVINNLLLNASIASNENAPGADEFLPVLIYVTIKANPPQLHSNLLYIQRYRRESKLVGEAAYFFTNILSAESFISNIDAKSISLDEAEFEKNMESARAR 262
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------VPS9  PDB: C:102-246 UniProt: 102-246                                                                                                            ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2efc C  17 MRKPSAGDFVKSIKSFIVSFSNNAPDPEKDCAMVQEFFSKMEAAFRAHPLWSGCSEEELDSAGDGLEKYVMTKLFTRVFASNTEEVIADEKLFQKMSLVQQFISPENLDIQPTFQNESSWLLAQKELQKINMYKAPRDKLVCILNCCKVINNLLLNASIASNENAPGADEFLPVLIYVTIKANPPQLHSNLLYIQRYRRESKLVGEAAYFFTNILSAESFISNIDAKSISLDEAEFEKNMESARAR 262
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256

Chain D from PDB  Type:PROTEIN  Length:165
 aligned with RAF2B_ARATH | Q9SN68 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:165
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167     
          RAF2B_ARATH     8 SINAKLVLLGDVGAGKSSLVLRFVKDQFVEFQESTIGAAFFSQTLAVNDATVKFEIWDTAGQERYHSLAPMYYRGAAAAIIVFDVTNQASFERAKKWVQELQAQGNPNMVMALAGNKSDLLDARKVTAEDAQTYAQENGLFFMETSAKTATNVKEIFYEIARRLP 172
               SCOP domains d2efcd_ D: automated matches                                                                                                                                          SCOP domains
               CATH domains 2efcD00 D:8-172 P-loop containing nucleotide triphosphate hydrolases                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh.............eeeeee......eeeeeee...hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhh..eeee.......hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2efc D   8 SINAKLVLLGDVGAGKSSLVLRFVKDQFVEFQESTIGAAFFSQTLAVNDATVKFEIWDTAGQERYHSLAPMYYRGAAAAIIVFDVTNQASFERAKKWVQELQAQGNPNMVMALAGNKSDLLDARKVTAEDAQTYAQENGLFFMETSAKTATNVKEIFYEIARRLP 172
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167

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 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: automated matches (173)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (9)

1a	d2efcb_	B:
1b	d2efcd_	D:

Asymmetric 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)

Thale cress (Arabidopsis thaliana) (10)

1a	2efcB00	B:8-172
1b	2efcD00	D:8-172

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

Asymmetric Unit(hide GO term definitions)

Chain A,C (VPS9A_ARATH | Q9LT31)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0005089	Rho guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. 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: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:0000919	cell plate assembly	The process of assembly, maturation, and growth of the cell plate to the cell periphery in cells that divide by cell plate formation; often involves deposition of cell wall material in and around the phragmoplast.
	GO:0042546	cell wall biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall. Includes biosynthesis of constituent macromolecules, such as proteins and polysaccharides, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. A cell wall is the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0009793	embryo development ending in seed dormancy	The process whose specific outcome is the progression of the embryo over time, from zygote formation to the end of seed dormancy. An example of this process is found in Arabidopsis thaliana.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0048528	post-embryonic root development	The process whose specific outcome is the progression of the post-embryonic root over time, from its formation to the mature structure.
cellular component
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B,D (RAF2B_ARATH | Q9SN68)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	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:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	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.
cellular component
	GO:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0031901	early endosome membrane	The lipid bilayer surrounding an early endosome.
	GO:0030139	endocytic vesicle	A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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:0005774	vacuolar membrane	The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
	GO:0005773	vacuole	A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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	2efc
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	VPS9A_ARATH \| Q9LT31
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	RAF2B_ARATH \| Q9SN68	:	2efd 2efe 2efh 4g01
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Description

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Ligands, Modified Residues, Ions (1, 2)

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