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(-) Description

Title :  SOLUTION STRUCTURE OF RASGRP2 EF HANDS BOUND TO CALCIUM
 
Authors :  J. Kuriyan, J. Iwig, Y. Vercoulen, R. Das, T. Barros, A. Limnander, Y. Ch J. Pelton, D. Wemmer, J. Roose
Date :  24 Jun 13  (Deposition) - 21 Aug 13  (Release) - 21 Aug 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
NMR Structure *:  A  (1x)
Keywords :  Protein, Ef Hand, Calcium-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. S. Iwig, Y. Vercoulen, R. Das, T. Barros, A. Limnander, Y. Che, J. G. Pelton, D. E. Wemmer, J. P. Roose, J. Kuriyan
Structural Analysis Of Autoinhibition In The Ras-Specific Exchange Factor Rasgrp1.
Elife V. 2 00813 2013
PubMed-ID: 23908768  |  Reference-DOI: 10.7554/ELIFE.00813

(-) Compounds

Molecule 1 - RAS GUANYL-RELEASING PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPSMT3
    GeneRASGRP2, CDC25L, MCG7
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCALCIUM AND DAG-REGULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR I, CALDAG-GEFI, CDC25-LIKE PROTEIN, HCDC25L, F25B3.3 KINASE-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  1
NMR Structure (10x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2MA2)

(-) Sites  (0, 0)

(no "Site" information available for 2MA2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2MA2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2MA2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038257G493AGRP2_HUMANPolymorphism2301562AG493A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038257G493AGRP2_HUMANPolymorphism2301562AG493A

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

(-) PROSITE Motifs  (2, 4)

NMR Structure (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.GRP2_HUMAN426-461
463-490
  2A:426-461
A:463-490
2EF_HAND_1PS00018 EF-hand calcium-binding domain.GRP2_HUMAN439-451
468-480
  2A:439-451
A:468-480
NMR Structure * (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.GRP2_HUMAN426-461
463-490
  2A:426-461
A:463-490
2EF_HAND_1PS00018 EF-hand calcium-binding domain.GRP2_HUMAN439-451
468-480
  2A:439-451
A:468-480

(-) Exons   (0, 0)

(no "Exon" information available for 2MA2)

(-) 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:81
 aligned with GRP2_HUMAN | Q7LDG7 from UniProtKB/Swiss-Prot  Length:609

    Alignment length:81
                                   426       436       446       456       466       476       486       496 
           GRP2_HUMAN   417 KLDQALVVEHIEKMVESVFRNFDVDGDGHISQEEFQIIRGNFPYLSAFGDLDQNQDGCISREEMVSYFLRSSSVLGGRMGF 497
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh........hhhhhhhhh.......hhhhhh.......hhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------A---- SAPs(SNPs)
                PROSITE (1) ---------EF_HAND_2  PDB: A:426-461           -EF_HAND_2  PDB: A:463-490   ------- PROSITE (1)
                PROSITE (2) ----------------------EF_HAND_1    ----------------EF_HAND_1    ----------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------- Transcript
                 2ma2 A 417 KLDQALVVEHIEKMVESVFRNFDVDGDGHISQEEFQIIRGNFPYLSAFGDLDQNQDGCISREEMVSYFLRSSSVLGGRMGF 497
                                   426       436       446       456       466       476       486       496 

   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  (0, 0)

(no "SCOP Domain" information available for 2MA2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2MA2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2MA2)

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (GRP2_HUMAN | Q7LDG7)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0019992    diacylglycerol binding    Interacting selectively and non-covalently with diacylglycerol, a diester of glycerol and two fatty acids.
    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:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0071277    cellular response to calcium ion    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 calcium ion stimulus.
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0001558    regulation of cell growth    Any process that modulates the frequency, rate, extent or direction of cell growth.
    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.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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(-) Related Entries Specified in the PDB File

4l9m RELATED ID: 19319 RELATED DB: BMRB