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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN NRAS GTPASE BOUND WITH GDP
 
Authors :  L. Nedyalkova, Y. Tong, W. Tempel, L. Shen, P. Loppnau, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  28 Mar 08  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics Consortium, Sgc, Gtpase, Gdp, Oncogene, Disease Mutation, Golgi Apparatus, Gtp-Binding, Lipoprotein, Membrane, Methylation, Nucleotide-Binding, Palmitate, Prenylation, Proto-Oncogene, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Nedyalkova, Y. Tong, W. Tempel, L. Shen, P. Loppnau, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Human Nras Gtpase Bound With Gdp.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GTPASE NRAS
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-CODONPLUS(DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-172
    GeneNRAS, HRAS1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTRANSFORMING PROTEIN N-RAS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG4Ligand/IonMAGNESIUM ION
3UNX8Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:17 , HOH A:226 , HOH A:265 , HOH A:279 , HOH A:282BINDING SITE FOR RESIDUE MG A 202
02AC2SOFTWAREGLY A:48 , HOH A:247 , HOH A:249 , HOH A:250 , HOH A:252 , HOH A:278BINDING SITE FOR RESIDUE MG A 203
03AC3SOFTWAREASP A:38 , HOH A:280 , HOH A:283 , HOH A:284 , HOH A:294BINDING SITE FOR RESIDUE MG A 204
04AC4SOFTWAREHOH A:231 , HOH A:245BINDING SITE FOR RESIDUE MG A 205
05AC5SOFTWAREGLY A:13 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , ASP A:30 , TYR A:32 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , HOH A:221 , HOH A:235 , HOH A:270 , HOH A:273 , HOH A:279 , HOH A:282 , HOH A:290 , HOH A:291BINDING SITE FOR RESIDUE GDP A 201
06AC6SOFTWAREASP A:47 , ARG A:102BINDING SITE FOR RESIDUE UNX A 206
07AC7SOFTWARELEU A:6 , ASP A:54BINDING SITE FOR RESIDUE UNX A 207
08AC8SOFTWAREGLY A:10 , THR A:58 , TYR A:96 , HOH A:234 , HOH A:236BINDING SITE FOR RESIDUE UNX A 208
09AC9SOFTWAREGLY A:10 , ALA A:11 , SER A:89BINDING SITE FOR RESIDUE UNX A 209
10BC1SOFTWAREGLU A:31 , ARG A:149 , GLU A:153 , HOH A:219BINDING SITE FOR RESIDUE UNX A 200
11BC2SOFTWARESER A:87 , LYS A:88 , THR A:124 , HOH A:217BINDING SITE FOR RESIDUE UNX A 211
12BC3SOFTWAREASN A:94 , LEU A:95 , HOH A:233BINDING SITE FOR RESIDUE UNX A 212
13BC4SOFTWAREASP A:154 , ARG A:161BINDING SITE FOR RESIDUE UNX A 213

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CON)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CON)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

Asymmetric/Biological Unit (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021194G12CRASN_HUMANUnclassified121913250AG12C
2UniProtVAR_071129G12DRASN_HUMANDisease (JMML)121913237AG12D
3UniProtVAR_063084G13DRASN_HUMANDisease (RALD)121434596AG13D
4UniProtVAR_006845G13RRASN_HUMANDisease (CMNS)121434595AG13R
5UniProtVAR_071130P34LRASN_HUMANDisease (KNEN)397514553AP34L
6UniProtVAR_063085T50IRASN_HUMANDisease (NS6)267606921AT50I
7UniProtVAR_063086G60ERASN_HUMANDisease (NS6)267606920AG60E

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RASPS51421 small GTPase Ras family profile.RASN_HUMAN1-189  1A:1-167

(-) Exons   (0, 0)

(no "Exon" information available for 3CON)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:156
 aligned with RASN_HUMAN | P01111 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
           RASN_HUMAN     1 MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYR 167
               SCOP domains d3cona_ A: automated matches                                                                                                                                            SCOP domains
               CATH domains 3conA00 A:1-167 P-loop containing nucleotide triphosphate hy           drolases                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee...-----------.....eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) -----------CD--------------------L---------------I---------E----------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------DR---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE RAS  PDB: A:1-167 UniProt: 1-189                                                                                                                                        PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3con A   1 MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG-----------MRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYR 167
                                    10        20        30        40        50        60         - |      80        90       100       110       120       130       140       150       160       
                                                                                      60          72                                                                                               

   Legend:   → Mismatch (orange background)
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  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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CON)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RASN_HUMAN | P01111)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0038128    ERBB2 signaling pathway    A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.
    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: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: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:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0072600    establishment of protein localization to Golgi    The directed movement of a protein to a specific location in the Golgi apparatus.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    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:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RASN_HUMAN | P011112n9c 5uhv

(-) Related Entries Specified in the PDB File

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