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(-) Description

Title :  CRYSTAL STRUCTURE OF M-RAS IN COMPLEX WITH GDP
 
Authors :  M. Ye, F. Shima, S. Muraoka, J. Liao, H. Okamoto, M. Yamamoto, A. Tamura, N. Yagi, T. Ueki, T. Kataoka
Date :  12 Apr 05  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Gtp-Binding, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ye, F. Shima, S. Muraoka, J. Liao, H. Okamoto, M. Yamamoto, A. Tamura, N. Yagi, T. Ueki, T. Kataoka
Crystal Structure Of M-Ras Reveals A Gtp-Bound "Off" State Conformation Of Ras Family Small Gtpases
J. Biol. Chem. V. 280 31267 2005
PubMed-ID: 15994326  |  Reference-DOI: 10.1074/JBC.M505503200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN M-RAS
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-178
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: RAS-RELATED PROTEIN R-RAS3, MUSCLE AND MICROSPIKES RAS, X-RAS, GTPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:27 , GDP A:1179 , HOH A:1181 , HOH A:1182 , HOH A:1183 , HOH A:1184BINDING SITE FOR RESIDUE MG A 1180
2AC2SOFTWAREGLY A:23 , VAL A:24 , GLY A:25 , LYS A:26 , SER A:27 , ALA A:28 , PHE A:38 , PRO A:40 , ASP A:41 , TYR A:42 , ASN A:126 , LYS A:127 , ASP A:129 , LEU A:130 , SER A:156 , ALA A:157 , MG A:1180 , HOH A:1181 , HOH A:1182 , HOH A:1184 , HOH A:1190 , HOH A:1202 , HOH A:1218 , HOH A:1229 , HOH A:1256 , HOH A:1277 , HOH A:1306BINDING SITE FOR RESIDUE GDP A 1179

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X1R)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:159 -Pro A:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X1R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X1R)

(-) Exons   (0, 0)

(no "Exon" information available for 1X1R)

(-) 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:169
 aligned with RASM_MOUSE | O08989 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:169
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           RASM_MOUSE    10 NLPTYKLVVVGDGGVGKSALTIQFFQKIFVPDYDPTIEDSYLKHTEIDNQWAILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTRDQGKEMATKYNIPYIETSAKDPPLNVDKTFHDLVRVIRQQ 178
               SCOP domains d1x1ra1 A:10-178 Ras-related protein M-Ras (XRas)                                                                                                                         SCOP domains
               CATH domains 1x1rA00 A:10-178 P-loop containing nucleotide triphosphate hydrolases                                                                                                     CATH domains
               Pfam domains -----Ras-1x1rA01 A:15-177                                                                                                                                               - Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee...hhhhh.hhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee..........hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x1r A  10 NLPTYKLVVVGDGGVGKSALTIQFFQKIFVPDYDPTIEDSYLKHTEIDNQWAILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTRDQGKEMATKYNIPYIETSAKDPPLNVDKTFHDLVRVIRQQ 178
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: Ras (176)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RASM_MOUSE | O08989)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0030742    GTP-dependent 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) using energy from the hydrolysis of GTP.
    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.
biological process
    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: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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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
        RASM_MOUSE | O08989: 1x1s 3kko 3kkp 3kkq 3pir 3pit

(-) Related Entries Specified in the PDB File

1x1s M-RAS IN COMPLEX WITH GPPNHP