2D86 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF THE CH DOMAIN FROM HUMAN VAV-3 PROTEIN

Authors :   T. Tomizawa, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   02 Dec 05 (Deposition) - 02 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   All Alpha, Calponin Homology Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Tomizawa, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The Ch Domain From Human Vav-3 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - VAV-3 PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P050404-11
	Expression System Vector Type	:	PLASMID
	Fragment	:	CH DOMAIN
	Gene	:	VAV3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2D86)

(no "Site" information available for 2D86)

(no "SS Bond" information available for 2D86)

(no "Cis Peptide Bond" information available for 2D86)

(no "SAP(SNP)/Variant" information available for 2D86)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CH	PS50021	Calponin homology domain profile.	VAV3_HUMAN	1-119	1	A:8-126

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000370056	1a	ENSE00001894713	chr1:108507766-108507288	479	VAV3_HUMAN	1-68	68	1	A:8-75	68
1.3	ENST00000370056	3	ENSE00001671942	chr1:108417639-108417523	117	VAV3_HUMAN	69-107	39	1	A:76-114	39
1.7	ENST00000370056	7	ENSE00001261464	chr1:108322114-108322056	59	VAV3_HUMAN	108-127	20	1	A:115-134	20
1.9	ENST00000370056	9	ENSE00001261458	chr1:108319918-108319853	66	VAV3_HUMAN	127-149	23	1	A:134-143	10
1.10	ENST00000370056	10	ENSE00000998251	chr1:108315465-108315357	109	VAV3_HUMAN	149-185	37	0	-	-
1.11b	ENST00000370056	11b	ENSE00000998263	chr1:108313350-108313258	93	VAV3_HUMAN	186-216	31	0	-	-
1.12	ENST00000370056	12	ENSE00001261509	chr1:108311131-108311063	69	VAV3_HUMAN	217-239	23	0	-	-
1.13b	ENST00000370056	13b	ENSE00000998260	chr1:108309172-108309069	104	VAV3_HUMAN	240-274	35	0	-	-
1.14	ENST00000370056	14	ENSE00000998254	chr1:108307797-108307698	100	VAV3_HUMAN	274-307	34	0	-	-
1.15	ENST00000370056	15	ENSE00000998258	chr1:108303501-108303406	96	VAV3_HUMAN	308-339	32	0	-	-
1.16	ENST00000370056	16	ENSE00000998243	chr1:108299951-108299883	69	VAV3_HUMAN	340-362	23	0	-	-
1.17	ENST00000370056	17	ENSE00000998240	chr1:108298135-108298049	87	VAV3_HUMAN	363-391	29	0	-	-
1.18	ENST00000370056	18	ENSE00000998242	chr1:108293824-108293739	86	VAV3_HUMAN	392-420	29	0	-	-
1.19a	ENST00000370056	19a	ENSE00000998262	chr1:108292216-108292084	133	VAV3_HUMAN	420-464	45	0	-	-
1.20	ENST00000370056	20	ENSE00000998256	chr1:108291699-108291590	110	VAV3_HUMAN	465-501	37	0	-	-
1.21	ENST00000370056	21	ENSE00000998249	chr1:108247683-108247582	102	VAV3_HUMAN	501-535	35	0	-	-
1.22	ENST00000370056	22	ENSE00000998255	chr1:108247272-108247172	101	VAV3_HUMAN	535-569	35	0	-	-
1.23c	ENST00000370056	23c	ENSE00000998248	chr1:108231028-108231003	26	VAV3_HUMAN	569-577	9	0	-	-
1.25	ENST00000370056	25	ENSE00000998266	chr1:108226155-108226110	46	VAV3_HUMAN	578-593	16	0	-	-
1.30	ENST00000370056	30	ENSE00000912776	chr1:108185377-108185241	137	VAV3_HUMAN	593-638	46	0	-	-
1.31b	ENST00000370056	31b	ENSE00000958099	chr1:108160254-108160189	66	VAV3_HUMAN	639-660	22	0	-	-
1.32a	ENST00000370056	32a	ENSE00000958100	chr1:108152587-108152553	35	VAV3_HUMAN	661-672	12	0	-	-
1.34b	ENST00000370056	34b	ENSE00000958101	chr1:108145785-108145669	117	VAV3_HUMAN	672-711	40	0	-	-
1.35	ENST00000370056	35	ENSE00000998246	chr1:108145106-108145019	88	VAV3_HUMAN	711-740	30	0	-	-
1.36b	ENST00000370056	36b	ENSE00000998252	chr1:108138963-108138834	130	VAV3_HUMAN	741-784	44	0	-	-
1.38	ENST00000370056	38	ENSE00000998244	chr1:108116820-108116669	152	VAV3_HUMAN	784-834	51	0	-	-
1.39f	ENST00000370056	39f	ENSE00001902342	chr1:108115994-108113782	2213	VAV3_HUMAN	835-847	13	0	-	-

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

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:143
 aligned with VAV3_HUMAN | Q9UKW4 from UniProtKB/Swiss-Prot  Length:847

    Alignment length:143
                                   1                                                                                                                                       
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133   
           VAV3_HUMAN     - -------MEPWKQCAQWLIHCKVLPTNHRVTWDSAQVFDLAQTLRDGVLLCQLLNNLRAHSINLKEINLRPQMSQFLCLKNIRTFLTACCETFGMRKSELFEAFDLFDVRDFGKVIETLSRLSRTPIALATGIRPFPTEESIN 136
               SCOP domains d2d86a_ A: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhh....hhhhh......hhhhhhhhhhhhhhhhhhh.........hhhhhhh...hhhhhhhhhhhh...hhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------CH  PDB: A:8-126 UniProt: 1-119                                                                                        ----------------- PROSITE
           Transcript 1 (1) -------Exon 1.1a  PDB: A:8-75 UniProt: 1-68                                Exon 1.3  PDB: A:76-114 UniProt: 69-107Exon 1.7            --------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------Exon 1.9   Transcript 1 (2)
                 2d86 A   1 GSSGSSGMEPWKQCAQWLIHCKVLPTNHRVTWDSAQVFDLAQTLRDGVLLCQLLNNLRAHSINLKEINLRPQMSQFLCLKNIRTFLTACCETFGMRKSELFEAFDLFDVRDFGKVIETLSRLSRTPIALATGIRPFPSGPSSG 143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: CH domain-like (55)

Superfamily: Calponin-homology domain, CH-domain (53)

Family: automated matches (25)

Protein domain: automated matches (25)

Human (Homo sapiens) [TaxId: 9606] (23)

d2d86a_

(no "CATH Domain" information available for 2D86)

(no "Pfam Domain" information available for 2D86)

NMR Structure(hide GO term definitions)

Chain A (VAV3_HUMAN | Q9UKW4)

molecular function
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0030676	Rac guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rac 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: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:0005070	SH3/SH2 adaptor activity	Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
	GO:0005154	epidermal growth factor receptor binding	Interacting selectively and non-covalently with the epidermal growth factor receptor.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0038095	Fc-epsilon receptor signaling pathway	A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
	GO:0038096	Fc-gamma receptor signaling pathway involved in phagocytosis	An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	GO:0030031	cell projection assembly	Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0048013	ephrin receptor signaling pathway	The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
	GO:0007229	integrin-mediated signaling pathway	A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	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:0030032	lamellipodium assembly	Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
	GO:0030593	neutrophil chemotaxis	The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
	GO:0030168	platelet activation	A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
	GO:0030890	positive regulation of B cell proliferation	Any process that activates or increases the rate or extent of B cell proliferation.
	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:0045785	positive regulation of cell adhesion	Any process that activates or increases the frequency, rate or extent of cell adhesion.
	GO:0043552	positive regulation of phosphatidylinositol 3-kinase activity	Any process that activates or increases the frequency, rate or extent of phosphatidylinositol 3-kinase activity.
	GO:0009967	positive regulation of signal transduction	Any process that activates or increases the frequency, rate or extent of signal transduction.
	GO:0043087	regulation of GTPase activity	Any process that modulates the rate of GTP hydrolysis by a GTPase.
	GO:0035023	regulation of Rho protein signal transduction	Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
	GO:0008361	regulation of cell size	Any process that modulates the size of a cell.
	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:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	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:0048010	vascular endothelial growth factor receptor signaling pathway	Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0006906	vesicle fusion	Fusion of the membrane of a transport vesicle with its target membrane.
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.
	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: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.

NMR Structure
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