2NTY - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ROP4-GDP-PRONE8

Authors :   C. Thomas, I. Fricke, A. Scrima, A. Berken, A. Wittinghofer

Date :   08 Nov 06 (Deposition) - 23 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Complex Of Prone-Gef With Rop Substrate, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Thomas, I. Fricke, A. Scrima, A. Berken, A. Wittinghofer
Structural Evidence For A Common Intermediate In Small G Protein-Gef Reactions
Mol. Cell V. 25 141 2007
PubMed-ID: 17218277 | Reference-DOI: 10.1016/J.MOLCEL.2006.11.023
(for further references see the PDB file header)

Molecule 1 - EMB\|CAB41934.1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 76-440 BASED ON THE DATABASE NUMBERING
	Gene	:	AT3G24620
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Strain	:	COLUMBIA
	Synonym	:	PRONE8

Molecule 2 - RAC-LIKE GTP-BINDING PROTEIN ARAC5
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T-1
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-180
	Gene	:	ATU52350
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Strain	:	COLUMBIA
	Synonym	:	GTPASE PROTEIN ROP4

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA C:16 , GLY C:18 , LYS C:19 , THR C:20 , CYS C:21 , LYS C:119 , ASP C:121 , SER C:159 , SER C:160 , LYS C:161	BINDING SITE FOR RESIDUE GDP C 1200
2	AC2	SOFTWARE	ASP D:14 , ALA D:16 , VAL D:17 , GLY D:18 , LYS D:19 , THR D:20 , CYS D:21 , PHE D:31 , ALA D:62 , LYS D:119 , ASP D:121 , LEU D:122 , SER D:159 , SER D:160 , LYS D:161	BINDING SITE FOR RESIDUE GDP D 2200

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:24	-	Glu A:25

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

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

(no "Exon" information available for 2NTY)

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:332
 aligned with ROGF8_ARATH | Q9LV40 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:354
                                    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    
          ROGF8_ARATH    85 DMEMMKDRFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQTKLQPMPQDRQARWKKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIMVTRQRGDLLMNIPALRKLDAMLIDTLDNFRGHNEFWYVSRDSEEGQQARNDRTNDKWWLPPVKVPPGGLSEPSRRMLYFQKDSVTQVQKAAMAINAQVLSEMEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAMLDMSTEHKVLDLKNRIEASVVIWKRKLHTKDTKSSWGSAVSLEKRELFEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVMSRIEDVLYTDTLALKQTL 438
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.......ee....hhhhhh.---.hhhhh....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhh....hhhhhhhhhhhhhhhhhhhh.-------------------hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nty A  10 DMEMMKDRFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQTKLQPMPQDRQARWKKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIMVTRQRGDLLMNIPALRKLDAMLIDTLDNFRGHNEFWYVSRDSEEGQQA---RTNDKWWLPPVKVPPGGLSEPSRRMLYFQKDSVTQVQKAAMAINAQVLSEMEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAMLDMSTEHKVLDLKNRIEASVVIWKR-------------------RELFEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVMSRIEDVLYTDTLALKQTL 363
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149|   |  159       169       179       189       199       209       219       229       239       249       259        |-         -       289       299       309       319       329       339       349       359    
                                                                                                                                                                      150 154                                                                                                               268                 288

Chain B from PDB  Type:PROTEIN  Length:337
 aligned with ROGF8_ARATH | Q9LV40 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:356
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433      
          ROGF8_ARATH    84 ADMEMMKDRFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQTKLQPMPQDRQARWKKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIMVTRQRGDLLMNIPALRKLDAMLIDTLDNFRGHNEFWYVSRDSEEGQQARNDRTNDKWWLPPVKVPPGGLSEPSRRMLYFQKDSVTQVQKAAMAINAQVLSEMEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAMLDMSTEHKVLDLKNRIEASVVIWKRKLHTKDTKSSWGSAVSLEKRELFEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVMSRIEDVLYTDTLALKQTLL 439
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) PRONE-2ntyB01 B:9-362                                                                                                                                                                                                                                                                                                                                             -- Pfam domains (1)
           Pfam domains (2) PRONE-2ntyB02 B:9-362                                                                                                                                                                                                                                                                                                                                             -- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.......ee....hhhhhh-----.........ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh--------------...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nty B   9 ADMEMMKDRFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQTKLQPMPQDRQARWKKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIMVTRQRGDLLMNIPALRKLDAMLIDTLDNFRGHNEFWYVSRDSEEGQQ-----TNDKWWLPPVKVPPGGLSEPSRRMLYFQKDSVTQVQKAAMAINAQVLSEMEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAMLDMSTEHKVLDLKNRIEASVVIWKRK--------------SLEKRELFEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVMSRIEDVLYTDTLALKQTLL 364
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148|     |158       168       178       188       198       208       218       228       238       248       258       268|        -     | 288       298       308       318       328       338       348       358      
                                                                                                                                                                      149   155                                                                                                               269            284

Chain C from PDB  Type:PROTEIN  Length:173
 aligned with RAC5_ARATH | Q38937 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      
           RAC5_ARATH     4 SRFIKCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLRPLSYRGADVFILAFSLISKASYENVAKKWIPELRHYAPGVPIILVGTKLDLRDDKQFFIDHPGAVPITTNQGEELKKLIGSPIYIECSSKTQQNVKAVFDAAIKVVLQ 179
               SCOP domains d2ntyc_ C: automated matches                                                                                                                                                     SCOP domains
               CATH domains 2ntyC00 C:4-179 P-loop contain   ing nucleotide triphosphate hydrolases                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhh....---......eeeeeee..eeeeeeee....................eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhh......hhhhhhhhhhhh....eee.......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nty C   4 SRFIKCVTVGDGAVGKTCMLISYTSNTFPT---PTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLRPLSYRGADVFILAFSLISKASYENVAKKWIPELRHYAPGVPIILVGTKLDLRDDKQFFIDHPGAVPITTNQGEELKKLIGSPIYIECSSKTQQNVKAVFDAAIKVVLQ 179
                                    13        23        33   |    43        53        63        73        83        93       103       113       123       133       143       153       163       173      
                                                        33  37

Chain D from PDB  Type:PROTEIN  Length:172
 aligned with RAC5_ARATH | Q38937 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:175
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174     
           RAC5_ARATH     5 RFIKCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLRPLSYRGADVFILAFSLISKASYENVAKKWIPELRHYAPGVPIILVGTKLDLRDDKQFFIDHPGAVPITTNQGEELKKLIGSPIYIECSSKTQQNVKAVFDAAIKVVLQ 179
               SCOP domains d2ntyd_ D: automated matches                                                                                                                                                    SCOP domains
               CATH domains 2ntyD00 D:5-179 P-loop contai   ning nucleotide triphosphate hydrolases                                                                                                         CATH domains
           Pfam domains (1) ---Ras-2ntyD01 D:8-179                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) ---Ras-2ntyD02 D:8-179                                                                                                                                                          Pfam domains (2)
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh....---......eeeeeee..eeeeeeee.......hhhhh........eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhh......hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nty D   5 RFIKCVTVGDGAVGKTCMLISYTSNTFPT---PTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLRPLSYRGADVFILAFSLISKASYENVAKKWIPELRHYAPGVPIILVGTKLDLRDDKQFFIDHPGAVPITTNQGEELKKLIGSPIYIECSSKTQQNVKAVFDAAIKVVLQ 179
                                    14        24        |-  |     44        54        64        74        84        94       104       114       124       134       144       154       164       174     
                                                       33  37

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: automated matches (303)

Protein domain: automated matches (303)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (5)

1a	d2ntyc_	C:
1b	d2ntyd_	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)

Thale cress (Arabidopsis thaliana) (10)

1a	2ntyC00	C:4-179
1b	2ntyD00	D:5-179

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Ras (176)

Arabidopsis thaliana (Mouse-ear cress) (2)

1a	Ras-2ntyD01	D:8-179
1b	Ras-2ntyD02	D:8-179

Clan: no clan defined [family: PRONE] (3)

Family: PRONE (3)

Arabidopsis thaliana (Mouse-ear cress) (3)

2a	PRONE-2ntyB01	B:9-362
2b	PRONE-2ntyB02	B:9-362

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ROGF8_ARATH | Q9LV40)

molecular function
	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: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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
cellular component
	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.

Chain C,D (RAC5_ARATH | Q38937)

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).
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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.
	GO:0009524	phragmoplast	Fibrous structure (light microscope view) that arises between the daughter nuclei at telophase and within which the initial partition (cell plate), dividing the mother cell in two (cytokinesis), is formed. Appears at first as a spindle connected to the two nuclei, but later spreads laterally in the form of a ring. Consists of microtubules.
	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.

Asymmetric/Biological Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:24 - Glu A:25	[ RasMol ]

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	ROGF8_ARATH \| Q9LV40	:	2ntx 2wbl

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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