2YSQ - JenaLib

Title :   SOLUTION STRUCTURE OF THE SH3 DOMAIN FROM RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 9

Authors :   X. R. Qin, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   03 Apr 07 (Deposition) - 09 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Sh3 Domain; Cdc42 Guanine Nucleotide Exchange Factor (Gef) 9, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. R. Qin, F. Hayashi, S. Yokoyama
Solution Structure Of The Sh3 Domain From Rho Guanine Nucleotide Exchange Factor 9
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 9
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P050919-06
	Expression System Vector Type	:	PLASMID
	Fragment	:	SH3 DOMAIN
	Gene	:	ARHGEF9, KIAA0424
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	RAC/CDC42 GUANINE NUCLEOTIDE EXCHANGE FACTOR 9, COLLYBISTIN, PEM-2 HOMOLOG

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (3, 3)

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000253401	2b	ENSE00001865551	X:62974993-62974184	810	ARHG9_HUMAN	1-3	3	1	A:1-3	3
1.4	ENST00000253401	4	ENSE00001769376	X:62944591-62944412	180	ARHG9_HUMAN	4-63	60	1	A:4-63	60
1.5	ENST00000253401	5	ENSE00001698744	X:62926329-62926138	192	ARHG9_HUMAN	64-127	64	1	A:64-81 (gaps)	31
1.8	ENST00000253401	8	ENSE00001801635	X:62917184-62917005	180	ARHG9_HUMAN	128-187	60	0	-	-
1.9	ENST00000253401	9	ENSE00001618937	X:62898452-62898220	233	ARHG9_HUMAN	188-265	78	0	-	-
1.10a	ENST00000253401	10a	ENSE00000671866	X:62894047-62893918	130	ARHG9_HUMAN	265-308	44	0	-	-
1.11	ENST00000253401	11	ENSE00000869084	X:62885897-62885766	132	ARHG9_HUMAN	309-352	44	0	-	-
1.12	ENST00000253401	12	ENSE00000897813	X:62875617-62875374	244	ARHG9_HUMAN	353-434	82	0	-	-
1.13c	ENST00000253401	13c	ENSE00000869082	X:62863928-62863860	69	ARHG9_HUMAN	434-457	24	0	-	-
1.14d	ENST00000253401	14d	ENSE00001844608	X:62858089-62854847	3243	ARHG9_HUMAN	457-516	60	0	-	-

Sequences/Alignments

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:81
 aligned with ARHG9_HUMAN | O43307 from UniProtKB/Swiss-Prot  Length:516

    Alignment length:94
                                    10        20        30        40        50        60        70        80        90    
           ARHG9_HUMAN    1 MTLLITGDSIVSAEAVWDHVTMANRELAFKAGDVIKVLDASNKDWWWGQIDDEEGWFPASFVRLWVNQEDEVEEGPSDVQNGHLDPNSDCLCLG 94
               SCOP domains d2ysqa_ A: automated matches                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------SH3_1-2ysqA01 A:14-59                         ----------------------------------- Pfam domains
         Sec.struct. author ..........eeeee..................eeeeee.....eeeee....eeeee...eee.............--------...-----. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------A--------------------------------------- SAPs(SNPs)
                    PROSITE -------SH3  PDB: A:8-67 UniProt: 8-67                              --------------------------- PROSITE
               Transcript 1 1.2Exon 1.4  PDB: A:4-63 UniProt: 4-63                         Exon 1.5  PDB: A:64-81 (gaps)   Transcript 1
                  2ysq A  1 GSSGSSGDSIVSAEAVWDHVTMANRELAFKAGDVIKVLDASNKDWWWGQIDDEEGWFPASFVRLWVNQEDEVEEGSG--------PSS-----G 81
                                    10        20        30        40        50        60        70      |  -     | | -   |
                                                                                                       77       78 |    81
                                                                                                                  80

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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

NMR Structure(hide GO term definitions)

Chain A (ARHG9_HUMAN | O43307)

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.
biological process
	GO:0034220	ion transmembrane transport	A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0035023	regulation of Rho protein signal transduction	Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
	GO:0051056	regulation of small GTPase mediated signal transduction	Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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