2G0N - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF THE HUMAN RAC3 IN COMPLEX WITH GDP AND CHLORIDE

Authors :   E. Ugochukwu, X. Yang, Y. Zao, J. Elkins, C. Gileadi, N. Burgess, S. Cole O. Gileadi, O. Fedorov, G. Bunkoczi, M. Sundstrom, C. Arrowsmith, J. W A. Edwards, F. Von Delft, D. Doyle, Structural Genomics Consortiu

Date :   13 Feb 06 (Deposition) - 30 May 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Gtpase Rac3A, Small Gtp Binding Protein, P21 Rac, Ras-Related C3 Botulinum Toxin Substrate 3, Signalling Protein, Structural Genomics, Structural Genomics Consortium, Sgc, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Ugochukwu, X. Yang, Y. Zao, J. Elkins, C. Gileadi, N. Burgess, S. Colebrook, O. Gileadi, O. Fedorov, G. Bunkoczi, M. Sundstrom, C. Arrowsmith, J. Weigelt, A. Edwards, F. Von Delft, D. Doyle
The Crystal Structure Of The Human Rac3 In Complex With Gdp And Chloride
To Be Published
PubMed: search

Molecule 1 - RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21 (DE3)-R3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RAC3
	Gene	:	RAC3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	P21-RAC3

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR B:17 , GDP B:502 , HOH B:737 , HOH B:742 , HOH B:815 , HOH B:818	BINDING SITE FOR RESIDUE MG B 601
2	AC2	SOFTWARE	THR A:17 , GDP A:501 , HOH A:748 , HOH A:788 , HOH A:844 , HOH A:847	BINDING SITE FOR RESIDUE MG A 602
3	AC3	SOFTWARE	GLY B:12 , LYS B:16 , GLY B:60 , GLN B:61 , GDP B:502 , HOH B:815	BINDING SITE FOR RESIDUE CL B 701
4	AC4	SOFTWARE	GLY A:12 , LYS A:16 , GLY A:60 , GLN A:61 , GDP A:501 , HOH A:844	BINDING SITE FOR RESIDUE CL A 702
5	AC5	SOFTWARE	SER A:151	BINDING SITE FOR RESIDUE CL A 703
6	AC6	SOFTWARE	ALA A:13 , VAL A:14 , GLY A:15 , LYS A:16 , THR A:17 , CYS A:18 , PHE A:28 , ILE A:33 , LYS A:116 , ASP A:118 , LEU A:119 , SER A:158 , ALA A:159 , LEU A:160 , MG A:602 , CL A:702 , HOH A:718 , HOH A:727 , HOH A:796 , HOH A:798 , HOH A:844 , HOH A:847 , TYR B:64	BINDING SITE FOR RESIDUE GDP A 501
7	AC7	SOFTWARE	TYR A:64 , ALA B:13 , VAL B:14 , GLY B:15 , LYS B:16 , THR B:17 , CYS B:18 , PHE B:28 , ILE B:33 , LYS B:116 , ASP B:118 , LEU B:119 , SER B:158 , ALA B:159 , LEU B:160 , MG B:601 , CL B:701 , HOH B:706 , HOH B:724 , HOH B:742 , HOH B:803 , HOH B:818	BINDING SITE FOR RESIDUE GDP B 502

(no "SS Bond" information available for 2G0N)

(no "Cis Peptide Bond" information available for 2G0N)

(no "SAP(SNP)/Variant" information available for 2G0N)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHO	PS51420	small GTPase Rho family profile.	RAC3_HUMAN	1-176	2	A:1-176 B:1-176

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHO	PS51420	small GTPase Rho family profile.	RAC3_HUMAN	1-176	1	A:1-176 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHO	PS51420	small GTPase Rho family profile.	RAC3_HUMAN	1-176	1	- B:1-176

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000306897	1	ENSE00001289808	chr17:79989532-79989672	141	RAC3_HUMAN	1-12	12	2	A:1-12 B:1-12	12 12
1.2	ENST00000306897	2	ENSE00001328203	chr17:79990263-79990334	72	RAC3_HUMAN	12-36	25	2	A:12-36 B:12-36	25 25
1.3	ENST00000306897	3	ENSE00001164123	chr17:79990587-79990704	118	RAC3_HUMAN	36-75	40	2	A:36-75 B:36-75	40 40
1.4	ENST00000306897	4	ENSE00001164119	chr17:79990823-79990885	63	RAC3_HUMAN	76-96	21	2	A:76-96 B:76-96	21 21
1.5	ENST00000306897	5	ENSE00001779448	chr17:79991316-79991475	160	RAC3_HUMAN	97-150	54	2	A:97-150 B:97-150	54 54
1.6	ENST00000306897	6	ENSE00001314642	chr17:79991575-79992077	503	RAC3_HUMAN	150-192	43	2	A:150-178 B:150-178	29 29

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:179
 aligned with RAC3_HUMAN | P60763 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:179
                             1                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           RAC3_HUMAN     - -MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPHTPILLVGTKLDLRDDKDTIERLRDKKLAPITYPQGLAMAREIGSVKYLECSALTQRGLKTVFDEAIRAVLC 178
               SCOP domains d2g0na_ A: automated matches                                                                                                                                                        SCOP domains
               CATH domains 2g0nA00 A:0-178 P-loop containing nucleotide triphosphate hydrolases                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhhh............eeeeeeee..eeeeeeee....hhhhh.hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhh......hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RHO  PDB: A:1-176 UniProt: 1-176                                                                                                                                                -- PROSITE
           Transcript 1 (1) -Exon 1.1    -----------------------Exon 1.3  PDB: A:36-75 UniProt: 36-75   Exon 1.4  PDB: A:76-9Exon 1.5  PDB: A:97-150 UniProt: 97-150               ---------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.2  PDB: A:12-36   -----------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:150-178      Transcript 1 (2)
                 2g0n A   0 SMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPHTPILLVGTKLDLRDDKDTIERLRDKKLAPITYPQGLAMAREIGSVKYLECSALTQRGLKTVFDEAIRAVLG 178
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with RAC3_HUMAN | P60763 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
           RAC3_HUMAN     1 MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPHTPILLVGTKLDLRDDKDTIERLRDKKLAPITYPQGLAMAREIGSVKYLECSALTQRGLKTVFDEAIRAVLC 178
               SCOP domains d2g0nb_ B: automated matches                                                                                                                                                       SCOP domains
               CATH domains 2g0nB00 B:1-178 P-loop containing nucleotide triphosphate hydrolases                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh............eeeeeeee..eeeeeeee....hhhhh.hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhh.....hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RHO  PDB: B:1-176 UniProt: 1-176                                                                                                                                                -- PROSITE
           Transcript 1 (1) Exon 1.1    -----------------------Exon 1.3  PDB: B:36-75 UniProt: 36-75   Exon 1.4  PDB: B:76-9Exon 1.5  PDB: B:97-150 UniProt: 97-150               ---------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.2  PDB: B:12-36   -----------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: B:150-178      Transcript 1 (2)
                 2g0n B   1 MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPHTPILLVGTKLDLRDDKDTIERLRDKKLAPITYPQGLAMAREIGSVKYLECSALTQRGLKTVFDEAIRAVLG 178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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	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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

Human (Homo sapiens) [TaxId: 9606] (112)

1a	d2g0na_	A:
1b	d2g0nb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

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

Human (Homo sapiens) (413)

1a	2g0nA00	A:0-178
1b	2g0nB00	B:1-178

(no "Pfam Domain" information available for 2G0N)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RAC3_HUMAN | P60763)

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:0048306	calcium-dependent 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), in the presence of calcium.
	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:0030036	actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0030031	cell projection assembly	Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0021894	cerebral cortex GABAergic interneuron development	The process whose specific outcome is the progression of a cerebral cortex GABAergic interneuron over time, from initial commitment to its fate, to the fully functional differentiated cell.
	GO:0048873	homeostasis of number of cells within a tissue	Any biological process involved in the maintenance of the steady-state number of cells within a population of cells in a tissue.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0050905	neuromuscular process	Any process pertaining to the functions of the nervous and muscular systems of an organism.
	GO:0050885	neuromuscular process controlling balance	Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors.
	GO:0031175	neuron projection development	The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	GO:0033630	positive regulation of cell adhesion mediated by integrin	Any process that activates or increases the frequency, rate, or extent of cell adhesion mediated by integrin.
	GO:1900026	positive regulation of substrate adhesion-dependent cell spreading	Any process that activates or increases the frequency, rate or extent of substrate adhesion-dependent cell spreading.
	GO:0022604	regulation of cell morphogenesis	Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized.
	GO:0014041	regulation of neuron maturation	Any process that modulates the frequency, rate or extent of neuron maturation, the process leading to the attainment of the full functional capacity of a neuron. This process is independent of morphogenetic change.
	GO:0051056	regulation of small GTPase mediated signal transduction	Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
	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:0051932	synaptic transmission, GABAergic	The vesicular release of gamma-aminobutyric acid (GABA). from a presynapse, across a chemical synapse, the subsequent activation of GABA receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
cellular component
	GO:0071944	cell periphery	The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0012505	endomembrane system	A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0031941	filamentous actin	A two-stranded helical polymer of the protein actin.
	GO:0030426	growth cone	The migrating motile tip of a growing nerve cell axon or dendrite.
	GO:0030027	lamellipodium	A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	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.

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	RAC3_HUMAN \| P60763	:	2c2h 2ic5 2ov2 2qme

1mh1	SMALL G-PROTEIN

Description

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Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (6, 12)

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