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(-) Description

Title :  SOLUTION STRUCTURE OF THE SH2 DOMAIN OF HUMAN PROTEIN VAV-2
 
Authors :  H. Endo, F. Hayashi, M. Yoshida, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  20 Apr 06  (Deposition) - 03 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rho Family Guanine Nucleotide Exchange Factor, 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 :  H. Endo, F. Hayashi, M. Yoshida, S. Yokoyama
Solution Structure Of The Sh2 Domain Of Human Protein Vav-2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN VAV-2
    ChainsA
    EngineeredYES
    Expression System PlasmidP050620-24
    Expression System Vector TypePLASMID
    FragmentSH2 DOMAIN
    GeneVAV2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 2DLZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.VAV2_HUMAN586-652
816-877
  1-
A:118-118
2SH2PS50001 Src homology 2 (SH2) domain profile.VAV2_HUMAN673-767  1A:18-112

(-) Exons   (7, 7)

NMR Structure (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003718501cENSE00001894042chr9:136857432-136857197236VAV2_HUMAN1-68680--
1.2bENST000003718502bENSE00001694493chr9:136804341-136804225117VAV2_HUMAN69-107390--
1.6aENST000003718506aENSE00001134180chr9:136726554-13672649659VAV2_HUMAN108-127200--
1.7ENST000003718507ENSE00001096267chr9:136699462-13669939469VAV2_HUMAN127-150240--
1.8ENST000003718508ENSE00001051205chr9:136677338-136677236103VAV2_HUMAN150-184350--
1.9ENST000003718509ENSE00001649860chr9:136675327-13667531315VAV2_HUMAN185-18950--
1.10ENST0000037185010ENSE00001051207chr9:136674260-13667416299VAV2_HUMAN190-222330--
1.11ENST0000037185011ENSE00001051214chr9:136672448-13667238069VAV2_HUMAN223-245230--
1.12ENST0000037185012ENSE00001051220chr9:136671303-136671203101VAV2_HUMAN246-279340--
1.13ENST0000037185013ENSE00001051196chr9:136662931-136662832100VAV2_HUMAN279-312340--
1.14ENST0000037185014ENSE00001051198chr9:136661646-13666155196VAV2_HUMAN313-344320--
1.15ENST0000037185015ENSE00001051199chr9:136660858-13666079069VAV2_HUMAN345-367230--
1.16ENST0000037185016ENSE00001134002chr9:136656991-13665690587VAV2_HUMAN368-396290--
1.17ENST0000037185017ENSE00001096253chr9:136654465-13665438086VAV2_HUMAN397-425290--
1.18ENST0000037185018ENSE00001096259chr9:136653608-136653476133VAV2_HUMAN425-469450--
1.19ENST0000037185019ENSE00001682200chr9:136652382-13665236815VAV2_HUMAN470-47450--
1.20ENST0000037185020ENSE00001096247chr9:136651007-136650898110VAV2_HUMAN475-511370--
1.21ENST0000037185021ENSE00001096246chr9:136649540-136649439102VAV2_HUMAN511-545350--
1.22ENST0000037185022ENSE00001133992chr9:136648713-13664862589VAV2_HUMAN545-575310--
1.23ENST0000037185023ENSE00001656614chr9:136645832-13664581617VAV2_HUMAN575-58060--
1.25ENST0000037185025ENSE00001388876chr9:136645061-13664504022VAV2_HUMAN581-58880--
1.26ENST0000037185026ENSE00001096262chr9:136644011-136643884128VAV2_HUMAN588-630431A:1-55
1.27ENST0000037185027ENSE00001133974chr9:136642585-13664251175VAV2_HUMAN631-655251A:6-72
1.28ENST0000037185028ENSE00001096269chr9:136641202-13664115053VAV2_HUMAN656-673181A:8-1811
1.29ENST0000037185029ENSE00001096274chr9:136640173-136640057117VAV2_HUMAN673-712401A:18-5740
1.30ENST0000037185030ENSE00001096237chr9:136637168-13663708188VAV2_HUMAN712-741301A:57-8630
1.31ENST0000037185031ENSE00001096272chr9:136635623-136635500124VAV2_HUMAN742-783421A:87-11327
1.32ENST0000037185032ENSE00001096231chr9:136634625-13663453987VAV2_HUMAN783-812301A:114-1174
1.33ENST0000037185033ENSE00001096243chr9:136633718-136633564155VAV2_HUMAN812-863520--
1.34bENST0000037185034bENSE00001456304chr9:136629231-1366270162216VAV2_HUMAN864-878150--

(-) 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    
   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:118
 aligned with VAV2_HUMAN | P52735 from UniProtKB/Swiss-Prot  Length:878

    Alignment length:198
                                   631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811        
           VAV2_HUMAN   622 GDPESPWWEGRLVQTRKSGYFPSSSVKPCPVDGRPPISRPPSREIDYTAYPWFAGNMERQQTDNLLKSHASGTYLIRERPAEAERFAISIKFNDEVKHIKVVEKDNWIHITEAKKFDSLLELVEYYQCHSLKESFKQLDTTLKYPYKSRERSASRASSRSPASCASYNFSFLSPQGLSFASQGPSAPFWSVFTPRVIG 819
               SCOP domains d2dlz            a_                       A: automated matches                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------2dlzA01 A:11-112 SHC Adaptor Protein                                                                  ---------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....------------..----------------------....hhhhh..eee..hhhhhhhhhhhh....eeee........eeeeee....eeeeeeeee..eee........hhhhhhhhhh....................-----------------------------------....-----------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE SH3  PDB: - UniProt: 586-652   --------------------SH2  PDB: A:18-112 UniProt: 673-767                                                            ------------------------------------------------SH3  PROSITE
           Transcript 1 (1) Exon 1.26Exon 1.27  PDB: A:6-7    Exon 1.28         --------------------------------------Exon 1.30  PDB: A:57-86       Exon 1.31  PDB: A:87-113 UniProt: 742-783 ----------------------------1.33     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.29  PDB: A:18-57 UniProt: 673-712----------------------------------------------------------------------Exon 1.32  PDB: A:114-117     ------- Transcript 1 (2)
                 2dlz A   1 GSSGS------------SG----------------------SREIDYTAYPWFAGNMERQQTDNLLKSHASGTYLIRERPAEAERFAISIKFNDEVKHIKVVEKDNWIHITEAKKFDSLLELVEYYQCHSLKESFKQLDTTLKYPYS-----------------------------------GPSS-----------G 118
                                |    -       ||-         -         - |      16        26        36        46        56        66        76        86        96       106      |  -         -         -         -  |  |   -       |
                                5            6|                      8                                                                                                      113                                 114  |         118
                                              7                                                                                                                                                                    117            

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        VAV2_HUMAN | P527352dm1 2lnw 2lnx 4roj

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