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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   IDENTIFICATION AND STRUCTURAL BASIS FOR A NOVEL INTERACTION BETWEEN VAV2 AND ARAP3

Authors :   B. Wu, J. Zhang, J. Wu, Y. Shi

Date :   05 Jan 12 (Deposition) - 21 Nov 12 (Release) - 21 Nov 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)
NMR Structure *: A,B  (1x)

Keywords :   Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Wu, F. Wang, J. Zhang, Z. Zhang, L. Qin, J. Peng, F. Li, J. Liu, G. Lu, Q. Gong, X. Yao, J. Wu, Y. Shi
Identification And Structural Basis For A Novel Interaction Between Vav2 And Arap3.
J. Struct. Biol. V. 180 84 2012
PubMed-ID: 22750419 | Reference-DOI: 10.1016/J.JSB.2012.06.011

Molecule 1 - GUANINE NUCLEOTIDE EXCHANGE FACTOR VAV2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	VECTOR
	Fragment	:	UNP RESIDUES 659-771
	Gene	:	VAV2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	VAV-2

Molecule 2 - ARF-GAP WITH RHO-GAP DOMAIN, ANK REPEAT AND PH DOMAIN- CONTAINING PROTEIN 3
	Chains	:	B
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 1404-1412
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
	Synonym	:	CENTAURIN-DELTA-3, CNT-D3
	Synthetic	:	YES

		1	2
NMR Structure (20x)	:	A	B
NMR Structure * (1x)	:	A	B

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

NMR Structure * (1, 1)

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

(no "Site" information available for 2LNW)

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

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

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	VAV2_HUMAN	673-767	1	A:673-767

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	VAV2_HUMAN	673-767	1	A:673-767

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000371850	1c	ENSE00001894042	chr9:136857432-136857197	236	VAV2_HUMAN	1-68	68	0	-	-
1.2b	ENST00000371850	2b	ENSE00001694493	chr9:136804341-136804225	117	VAV2_HUMAN	69-107	39	0	-	-
1.6a	ENST00000371850	6a	ENSE00001134180	chr9:136726554-136726496	59	VAV2_HUMAN	108-127	20	0	-	-
1.7	ENST00000371850	7	ENSE00001096267	chr9:136699462-136699394	69	VAV2_HUMAN	127-150	24	0	-	-
1.8	ENST00000371850	8	ENSE00001051205	chr9:136677338-136677236	103	VAV2_HUMAN	150-184	35	0	-	-
1.9	ENST00000371850	9	ENSE00001649860	chr9:136675327-136675313	15	VAV2_HUMAN	185-189	5	0	-	-
1.10	ENST00000371850	10	ENSE00001051207	chr9:136674260-136674162	99	VAV2_HUMAN	190-222	33	0	-	-
1.11	ENST00000371850	11	ENSE00001051214	chr9:136672448-136672380	69	VAV2_HUMAN	223-245	23	0	-	-
1.12	ENST00000371850	12	ENSE00001051220	chr9:136671303-136671203	101	VAV2_HUMAN	246-279	34	0	-	-
1.13	ENST00000371850	13	ENSE00001051196	chr9:136662931-136662832	100	VAV2_HUMAN	279-312	34	0	-	-
1.14	ENST00000371850	14	ENSE00001051198	chr9:136661646-136661551	96	VAV2_HUMAN	313-344	32	0	-	-
1.15	ENST00000371850	15	ENSE00001051199	chr9:136660858-136660790	69	VAV2_HUMAN	345-367	23	0	-	-
1.16	ENST00000371850	16	ENSE00001134002	chr9:136656991-136656905	87	VAV2_HUMAN	368-396	29	0	-	-
1.17	ENST00000371850	17	ENSE00001096253	chr9:136654465-136654380	86	VAV2_HUMAN	397-425	29	0	-	-
1.18	ENST00000371850	18	ENSE00001096259	chr9:136653608-136653476	133	VAV2_HUMAN	425-469	45	0	-	-
1.19	ENST00000371850	19	ENSE00001682200	chr9:136652382-136652368	15	VAV2_HUMAN	470-474	5	0	-	-
1.20	ENST00000371850	20	ENSE00001096247	chr9:136651007-136650898	110	VAV2_HUMAN	475-511	37	0	-	-
1.21	ENST00000371850	21	ENSE00001096246	chr9:136649540-136649439	102	VAV2_HUMAN	511-545	35	0	-	-
1.22	ENST00000371850	22	ENSE00001133992	chr9:136648713-136648625	89	VAV2_HUMAN	545-575	31	0	-	-
1.23	ENST00000371850	23	ENSE00001656614	chr9:136645832-136645816	17	VAV2_HUMAN	575-580	6	0	-	-
1.25	ENST00000371850	25	ENSE00001388876	chr9:136645061-136645040	22	VAV2_HUMAN	581-588	8	0	-	-
1.26	ENST00000371850	26	ENSE00001096262	chr9:136644011-136643884	128	VAV2_HUMAN	588-630	43	0	-	-
1.27	ENST00000371850	27	ENSE00001133974	chr9:136642585-136642511	75	VAV2_HUMAN	631-655	25	0	-	-
1.28	ENST00000371850	28	ENSE00001096269	chr9:136641202-136641150	53	VAV2_HUMAN	656-673	18	1	A:659-673	15
1.29	ENST00000371850	29	ENSE00001096274	chr9:136640173-136640057	117	VAV2_HUMAN	673-712	40	1	A:673-712	40
1.30	ENST00000371850	30	ENSE00001096237	chr9:136637168-136637081	88	VAV2_HUMAN	712-741	30	1	A:712-741	30
1.31	ENST00000371850	31	ENSE00001096272	chr9:136635623-136635500	124	VAV2_HUMAN	742-783	42	1	A:742-771	30
1.32	ENST00000371850	32	ENSE00001096231	chr9:136634625-136634539	87	VAV2_HUMAN	783-812	30	0	-	-
1.33	ENST00000371850	33	ENSE00001096243	chr9:136633718-136633564	155	VAV2_HUMAN	812-863	52	0	-	-
1.34b	ENST00000371850	34b	ENSE00001456304	chr9:136629231-136627016	2216	VAV2_HUMAN	864-878	15	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:113
 aligned with VAV2_HUMAN | P52735 from UniProtKB/Swiss-Prot  Length:878

    Alignment length:113
                                   668       678       688       698       708       718       728       738       748       758       768   
          VAV2_HUMAN    659 SRPPSREIDYTAYPWFAGNMERQQTDNLLKSHASGTYLIRERPAEAERFAISIKFNDEVKHIKVVEKDNWIHITEAKKFDSLLELVEYYQCHSLKESFKQLDTTLKYPYKSRE  771
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhh....eeeee.....eeeeeeee....eeeeeeeee..eee........hhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------SH2  PDB: A:673-767 UniProt: 673-767                                                           ---- PROSITE
           Transcript 1 (1) Exon 1.28      --------------------------------------Exon 1.30  PDB: A:712-741     Exon 1.31  PDB: A:742-771      Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.29  PDB: A:673-712               ----------------------------------------------------------- Transcript 1 (2)
                2lnw A  659 SRPPSREIDYTAYPWFAGNMERQQTDNLLKSHASGTYLIRERPAEAERFAISIKFNDEVKHIKVVEKDNWIHITEAKKFDSLLELVEYYQCHSLKESFKQLDTTLKYPYKSRE  771
                                   668       678       688       698       708       718       728       738       748       758       768

Chain B from PDB  Type:PROTEIN  Length:9
 aligned with ARAP3_HUMAN | Q8WWN8 from UniProtKB/Swiss-Prot  Length:1544

    Alignment length:9
         ARAP3_HUMAN   1404 EEPVYEEVG 1412
               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 --------- Transcript
                2lnw B 1404 EEPVyEEVG 1412
                                |    
                                |    
                             1408-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 2LNW)

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

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

NMR Structure(hide GO term definitions)

Chain A (VAV2_HUMAN | P52735)

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: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: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:0048013	ephrin receptor signaling pathway	The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
	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: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: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: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:0030193	regulation of blood coagulation	Any process that modulates the frequency, rate or extent of blood coagulation.
	GO:0008361	regulation of cell size	Any process that modulates the size of a cell.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	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:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	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: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: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 (ARAP3_HUMAN | Q8WWN8)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005547	phosphatidylinositol-3,4,5-trisphosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-3,4,5-trisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3', 4' and 5' positions.
	GO:0043325	phosphatidylinositol-3,4-bisphosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions.
	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:0007010	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.
	GO:0035021	negative regulation of Rac protein signal transduction	Any process that stops, prevents, or reduces the frequency, rate or extent of Rac protein signal transduction.
	GO:0035024	negative regulation of Rho protein signal transduction	Any process that stops, prevents, or reduces the frequency, rate or extent of Rho protein signal transduction.
	GO:0030336	negative regulation of cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration 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:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	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: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: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.
	GO:0001726	ruffle	Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

NMR Structure
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	ARAP3_HUMAN \| Q8WWN8	:	2kg5 5jcp 5jd0
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Description

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