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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF THE VAV1 SH2 DOMAIN COMPLEXED WITH A TYROSINE-PHOSPHORYLATED PEPTIDE FROM SLP76

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

Date :   08 Apr 08 (Deposition) - 21 Apr 09 (Release) - 21 Apr 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)

Keywords :   Sh2 Domain, Protein-Peptide Complex, Phosphorylated Peptide Recognition, Phosphotyrosine Binding Domain, Signal Transduction, Guanine-Nucleotide Releasing Factor, Metal- Binding, Phorbol-Ester Binding, Phosphoprotein, Proto- Oncogene, Sh3 Domain, Zinc, Zinc-Finger, Signaling Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Kasai, M. Tanaka, S. Koshiba, T. Kigawa, S. Yokoyama
Solution Structure Of The Vav1 Sh2 Domain Complexed With A Tyrosine-Phosphorylated Peptide From Slp76
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROTO-ONCOGENE VAV
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL-FREE SYNTHESIS
	Expression System Vector	:	P040517-08
	Expression System Vector Type	:	VECTOR
	Fragment	:	SH2 DOMAIN, UNP RESIDUES 629-775
	Gene	:	VAV1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	E. COLI CELL FREE

Molecule 2 - 15-MERIC PEPTIDE FROM LYMPHOCYTE CYTOSOLIC PROTEIN 2
	Chains	:	B
	Engineered	:	YES
	Other Details	:	TYROSINE PHOSPHORYLATION SITE
	Other Details - Source	:	CHEMICAL SYNTHESIS
	Synonym	:	SH2 DOMAIN-CONTAINING LEUKOCYTE PROTEIN OF 76 KDA, SLP-76 TYROSINE PHOSPHOPROTEIN, SLP76
	Synthetic	:	YES


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

No.	Name	Count	Type	Full Name
1	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE

(no "Site" information available for 2ROR)

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

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

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051997	T	739	M	VAV_HUMAN	Polymorphism	36097961	A	T	96	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3	PS50002	Src homology 3 (SH3) domain profile.	VAV_HUMAN	617-660 782-842	1	A:7-18 -
2	SH2	PS50001	Src homology 2 (SH2) domain profile.	VAV_HUMAN	671-765	1	A:28-122

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000046794	1a	ENSE00002138597	chr5:169725231-169724538	694	LCP2_HUMAN	1-26	26	0	-	-
1.2	ENST00000046794	2	ENSE00000769343	chr5:169720376-169720314	63	LCP2_HUMAN	27-47	21	0	-	-
1.3a	ENST00000046794	3a	ENSE00000769339	chr5:169715020-169714974	47	LCP2_HUMAN	48-63	16	0	-	-
1.4a	ENST00000046794	4a	ENSE00000769324	chr5:169702864-169702799	66	LCP2_HUMAN	63-85	23	0	-	-
1.5	ENST00000046794	5	ENSE00000769295	chr5:169702355-169702324	32	LCP2_HUMAN	85-96	12	0	-	-
1.6a	ENST00000046794	6a	ENSE00000769292	chr5:169701342-169701305	38	LCP2_HUMAN	96-108	13	0	-	-
1.7a	ENST00000046794	7a	ENSE00000769288	chr5:169697921-169697723	199	LCP2_HUMAN	109-175	67	1	B:1-15	15
1.8	ENST00000046794	8	ENSE00000769287	chr5:169695486-169695389	98	LCP2_HUMAN	175-207	33	0	-	-
1.9c	ENST00000046794	9c	ENSE00000769283	chr5:169694079-169694013	67	LCP2_HUMAN	208-230	23	0	-	-
1.10	ENST00000046794	10	ENSE00000769281	chr5:169693895-169693812	84	LCP2_HUMAN	230-258	29	0	-	-
1.11	ENST00000046794	11	ENSE00001026289	chr5:169689996-169689971	26	LCP2_HUMAN	258-266	9	0	-	-
1.12	ENST00000046794	12	ENSE00001026292	chr5:169689865-169689846	20	LCP2_HUMAN	267-273	7	0	-	-
1.13	ENST00000046794	13	ENSE00000812801	chr5:169689746-169689639	108	LCP2_HUMAN	273-309	37	0	-	-
1.14	ENST00000046794	14	ENSE00000812800	chr5:169688141-169688111	31	LCP2_HUMAN	309-319	11	0	-	-
1.15	ENST00000046794	15	ENSE00001632768	chr5:169685882-169685870	13	LCP2_HUMAN	320-324	5	0	-	-
1.16b	ENST00000046794	16b	ENSE00000769273	chr5:169685170-169685041	130	LCP2_HUMAN	324-367	44	0	-	-
1.17b	ENST00000046794	17b	ENSE00000769269	chr5:169683579-169683530	50	LCP2_HUMAN	367-384	18	0	-	-
1.18	ENST00000046794	18	ENSE00000812799	chr5:169680217-169680123	95	LCP2_HUMAN	384-415	32	0	-	-
1.19	ENST00000046794	19	ENSE00000769265	chr5:169679515-169679438	78	LCP2_HUMAN	416-441	26	0	-	-
1.20b	ENST00000046794	20b	ENSE00000609392	chr5:169677889-169677734	156	LCP2_HUMAN	442-493	52	0	-	-
1.21c	ENST00000046794	21c	ENSE00002100375	chr5:169675823-169673241	2583	LCP2_HUMAN	494-533	40	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
	(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:138
 aligned with VAV_HUMAN | P15498 from UniProtKB/Swiss-Prot  Length:845

    Alignment length:171
                                   620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780 
            VAV_HUMAN   611 GAIGPFLRLNPGDIVELTKAEAEQNWWEGRNTSTNEIGWFPCNRVKPYVHGPPQDLSVHLWYAGPMERAGAESILANRSDGTFLVRQRVKDAAEFAISIKYNVEVKHIKIMTAEGLYRITEKKAFRGLTELVEFYQQNSLKDCFKSLDTTLQFPFKEPEKRTISRPAVGST 781
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------SH2-2rorA01 A:28-102                                                       ------------------------------------ Pfam domains
         Sec.struct. author ....-----...------...........----------------------...hhhhh.......hhhhhhhhhhhh......eee.......eeeeeee..eeeeeee................hhhhhhhhhh..hhhhh............................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------M------------------------------------------ SAPs(SNPs)
                    PROSITE ------SH3  PDB: A:7-18 UniProt: 617-660           ----------SH2  PDB: A:28-122 UniProt: 671-765                                                            ---------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ror A   1 GSSG-----SSG------KAEAEQNWWEG----------------------PPQDLSVHLWYAGPMERAGAESILANRSDGTFLVRQRVKDAAEFAISIKYNVEVKHIKIMTAEGLYRITEKKAFRGLTELVEFYQQNSLKDCFKSLDTTLQFPFKEPEKRTISRSGPSSG 138
                               |     5 |      |9        |-         -         - |      27        37        47        57        67        77        87        97       107       117       127       137 
                               4     5 7      8        18                     19

Chain B from PDB  Type:PROTEIN  Length:15
 aligned with LCP2_HUMAN | Q13094 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:15
                                   131     
           LCP2_HUMAN   122 GEDDGDYESPNEEEE 136
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ............... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
               Transcript 1 Exon 1.7a       Transcript 1
                 2ror B   1 GEDDGDyESPNEEEE  15
                                  | 10     
                                  7-PTR

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 '\|'

(no "SCOP Domain" information available for 2ROR)

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

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: SH2] (119)

Family: SH2 (119)

Homo sapiens (Human) (79)

SH2-2rorA01

A:28-102

NMR Structure(hide GO term definitions)

Chain A (VAV_HUMAN | P15498)

molecular function
	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: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:0046934	phosphatidylinositol-4,5-bisphosphate 3-kinase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+).
	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:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	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:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0042110	T cell activation	The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0030217	T cell differentiation	The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	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: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:0006909	phagocytosis	An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
	GO:0046854	phosphatidylinositol phosphorylation	The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
	GO:0048015	phosphatidylinositol-mediated signaling	A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	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: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:0045954	positive regulation of natural killer cell mediated cytotoxicity	Any process that activates or increases the frequency, rate or extent of natural killer cell mediated cytotoxicity.
	GO:0072593	reactive oxygen species metabolic process	The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
	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:0014066	regulation of phosphatidylinositol 3-kinase signaling	Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	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.
cellular component
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	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: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 B (LCP2_HUMAN | Q13094)

molecular function
	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: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:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0050663	cytokine secretion	The regulated release of cytokines from a cell. Cytokines are any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	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:0045576	mast cell activation	The change in morphology and behavior of a mast cell resulting from exposure to a cytokine, chemokine, soluble factor, or to (at least in mammals) an antigen which the mast cell has specifically bound via IgE bound to Fc-epsilonRI receptors.
	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:0045860	positive regulation of protein kinase activity	Any process that activates or increases the frequency, rate or extent of protein kinase activity.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0036398	TCR signalosome	A multi-protein complex containing at least the T-cell receptor complex and the LAT (linker for activation of T cells) scaffold protein. Also contains a variety of signaling proteins including co-receptors, kinases, phosphatases and adaptors such as CD8. Connects events on the plasma membrane to distal signaling cascades to ultimately modulate T cell biology.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	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:0044853	plasma membrane raft	A membrane raft that is part of the plasma membrane.

NMR Structure
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	LCP2_HUMAN \| Q13094	:	1h3h 1ywo 2eap
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