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(-) Description

Title :  SOLUTION STRUCTURE OF THE N-TERMINAL RAS-BINDING DOMAIN (RBD) IN HUMAN A-RAF KINASE
 
Authors :  C. Zhao, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Jan 05  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ras-Binding Domain (Rbd), Ubiquitin-Like Fold, A-Raf Kinase, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Zhao, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The N-Terminal Ras-Binding Domain (Rbd) In Human A-Raf Kinase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - A-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE
    ChainsA
    EC Number2.7.1.37
    EngineeredYES
    Expression System PlasmidP040712-12
    Expression System Vector TypePLASMID
    FragmentRAS-BINDING DOMAIN
    GeneARAF1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymA-RAF KINASE, A- RAF-1, PROTO-ONCOGENE PKS

 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 1WXM)

(-) Sites  (0, 0)

(no "Site" information available for 1WXM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WXM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WXM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WXM)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RBDPS50898 Ras-binding domain (RBD) profile.ARAF_HUMAN19-91  1A:8-80

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003770451aENSE00001832535X:47420516-47420650135ARAF_HUMAN-00--
1.2aENST000003770452aENSE00001093194X:47422308-47422462155ARAF_HUMAN1-32321A:1-21 (gaps)22
1.3ENST000003770453ENSE00000669305X:47422625-47422728104ARAF_HUMAN33-67351A:22-5635
1.4ENST000003770454ENSE00000669307X:47424196-47424298103ARAF_HUMAN67-101351A:56-8126
1.5aENST000003770455aENSE00000669309X:47424384-47424538155ARAF_HUMAN102-153520--
1.6bENST000003770456bENSE00001043758X:47424651-4742474999ARAF_HUMAN153-186341A:82-843
1.7ENST000003770457ENSE00001043742X:47426038-47426179142ARAF_HUMAN186-233481A:84-863
1.8ENST000003770458ENSE00000669315X:47426283-4742631028ARAF_HUMAN234-243100--
1.9ENST000003770459ENSE00000669317X:47426385-47426530146ARAF_HUMAN243-291490--
1.10ENST0000037704510ENSE00000669319X:47426629-47426831203ARAF_HUMAN292-359680--
1.11ENST0000037704511ENSE00000669321X:47428117-47428293177ARAF_HUMAN359-418600--
1.12ENST0000037704512ENSE00001740061X:47428386-4742843247ARAF_HUMAN418-434170--
1.13bENST0000037704513bENSE00001472613X:47428938-47429056119ARAF_HUMAN434-473400--
1.14aENST0000037704514aENSE00000669340X:47429292-47429423132ARAF_HUMAN474-517440--
1.15ENST0000037704515ENSE00000867024X:47430277-47430411135ARAF_HUMAN518-562450--
1.16bENST0000037704516bENSE00001936221X:47430722-47431299578ARAF_HUMAN563-606440--

(-) 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:86
 aligned with ARAF_HUMAN | P10398 from UniProtKB/Swiss-Prot  Length:606

    Alignment length:178
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
           ARAF_HUMAN    11 GAEPSRAVGTVKVYLPNKQRTVVTVRDGMSVYDSLDKALKVRGLNQDCCVVYRLIKGRKTVTAWDTAIAPLDGEELIVEVLEDVPLTMHNFVRKTFFSLAFCDFCLKFLFHGFRCQTCGYKFHQHCSSKVPTVCVDMSTNRQQFYHSVQDLSGGSRQHEAPSNRPLNELLTPQGPSPR 188
               SCOP domains --------d1wxma1 A:8-80 A-Raf proto-oncogene serine/threonine-protein kinase      ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------1wxmA01 A:9-79                                                         -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------RBD-1wxmA01 A:8-80                                                       ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-...eeeee.....eeeee.......hhhhhhhhh........eeeeee....eeee............eeeeee..-------------------------------------------------------------------------------------------..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------RBD  PDB: A:8-80 UniProt: 19-91                                          ------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a [INCOMPLETE]Exon 1.3  PDB: A:22-56             ----------------------------------Exon 1.5a  PDB: - UniProt: 102-153                  --------------------------------1.7 Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.4  PDB: A:56-81 [INCOMPLETE]---------------------------------------------------Exon 1.6b  PDB: A:82-84           -- Transcript 1 (2)
                 1wxm A   1 GSSGS-SGGTVKVYLPNKQRTVVTVRDGMSVYDSLDKALKVRGLNQDCCVVYRLIKGRKTVTAWDTAIAPLDGEELIVEVLS-------------------------------------------------------------------------------------------GPSSG  86
                                | |  9        19        29        39        49        59        69        79 |       -         -         -         -         -         -         -         -         -   |    
                                5 6                                                                         81                                                                                          82    

   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  (1, 1)

NMR Structure
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (ARAF_HUMAN | P10398)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0005057    signal transducer activity, downstream of receptor    Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    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:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0033138    positive regulation of peptidyl-serine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0032006    regulation of TOR signaling    Any process that modulates the frequency, rate or extent of TOR signaling.
    GO:0032434    regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that modulates the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    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.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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