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(-) Description

Title :  CRYSTAL STRUCTURE OF M-RAS P40D/D41E/L51R IN COMPLEX WITH GPPNHP
 
Authors :  S. Muraoka, F. Shima, J. Liao, Y. Ijiri, K. Matsumoto, M. Ye, T. Inoue, T.
Date :  06 Nov 09  (Deposition) - 16 Jun 10  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,P
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  P  (1x)
Keywords :  Gtp-Binding, Gtpase, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Shima, Y. Ijiri, S. Muraoka, J. Liao, M. Ye, M. Araki, K. Matsumoto, N. Yamamoto, T. Sugimoto, Y. Yoshikawa, T. Kumasaka, M. Yamamoto, A. Tamura, T. Kataoka
Structural Basis For Conformational Dynamics Of Gtp-Bound Ras Protein
J. Biol. Chem. V. 285 22696 2010
PubMed-ID: 20479006  |  Reference-DOI: 10.1074/JBC.M110.125161

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN M-RAS
    Chains: A, B, P
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: G DOMAIN, UNP RESIDUES 1-178
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: RAS-RELATED PROTEIN R-RAS3, MUSCLE AND MICROSPIKES RAS, X- RAS

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABP
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   P

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1GNP3Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG3Ligand/IonMAGNESIUM ION
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:22 , GLY A:23 , VAL A:24 , GLY A:25 , LYS A:26 , SER A:27 , ALA A:28 , PHE A:38 , VAL A:39 , ASP A:40 , GLU A:41 , TYR A:42 , PRO A:44 , THR A:45 , GLY A:70 , ASN A:126 , LYS A:127 , ASP A:129 , LEU A:130 , SER A:156 , ALA A:157 , MG A:180 , HOH A:1001 , HOH A:1002 , HOH A:1003 , HOH A:1004 , HOH A:1005 , HOH A:1053 , HOH A:1109 , HOH A:1127BINDING SITE FOR RESIDUE GNP A 179
2AC2SOFTWARESER A:27 , THR A:45 , GNP A:179 , HOH A:1001 , HOH A:1002BINDING SITE FOR RESIDUE MG A 180
3AC3SOFTWARELYS A:166 , HIS A:169 , ARG A:173 , HOH A:1113 , HOH A:1150BINDING SITE FOR RESIDUE SO4 A 181
4AC4SOFTWAREHOH A:1066 , GLY B:22 , GLY B:23 , VAL B:24 , GLY B:25 , LYS B:26 , SER B:27 , ALA B:28 , PHE B:38 , VAL B:39 , ASP B:40 , GLU B:41 , PRO B:44 , THR B:45 , GLY B:70 , ASN B:126 , LYS B:127 , ASP B:129 , LEU B:130 , SER B:156 , ALA B:157 , LYS B:158 , MG B:180 , HOH B:1001 , HOH B:1002 , HOH B:1003 , HOH B:1004 , HOH B:1009 , HOH B:1035BINDING SITE FOR RESIDUE GNP B 179
5AC5SOFTWARESER B:27 , THR B:45 , GNP B:179 , HOH B:1001 , HOH B:1002BINDING SITE FOR RESIDUE MG B 180
6AC6SOFTWARELYS B:166 , HIS B:169 , ARG B:173BINDING SITE FOR RESIDUE SO4 B 181
7AC7SOFTWAREGLY P:22 , GLY P:23 , VAL P:24 , GLY P:25 , LYS P:26 , SER P:27 , ALA P:28 , PHE P:38 , VAL P:39 , ASP P:40 , GLU P:41 , TYR P:42 , THR P:45 , GLY P:70 , ASN P:126 , LYS P:127 , ASP P:129 , LEU P:130 , SER P:156 , ALA P:157 , MG P:180 , HOH P:1001 , HOH P:1002 , HOH P:1003 , HOH P:1004 , HOH P:1018 , HOH P:1026BINDING SITE FOR RESIDUE GNP P 179
8AC8SOFTWARESER P:27 , THR P:45 , GNP P:179 , HOH P:1001 , HOH P:1002BINDING SITE FOR RESIDUE MG P 180
9AC9SOFTWARELYS P:166 , HIS P:169 , ARG P:173 , HOH P:1114BINDING SITE FOR RESIDUE SO4 P 181

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:159 -Pro A:160
2Asp B:159 -Pro B:160
3Asp P:159 -Pro P:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KKO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KKO)

(-) Exons   (0, 0)

(no "Exon" information available for 3KKO)

(-) Sequences/Alignments

Asymmetric 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 d3kkoa_ A: automated matches                                                                                                                                              SCOP domains
               CATH domains 3kkoA00 A:10-178 P-loop containing nucleotide triphosphate hydrolases                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee..........hhhhhhhhhhhh...eee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kko A  10 NLPTYKLVVVGDGGVGKSALTIQFFQKIFVDEYDPTIEDSYRKHTEIDNQWAILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTRDQGKEMATKYNIPYIETSAKDPPLNVDKTFHDLVRVIRQQ 178
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         


Chain B 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 d3kkob_ B: automated matches                                                                                                                                              SCOP domains
               CATH domains 3kkoB00 B:10-178 P-loop containing nucleotide triphosphate hydrolases                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kko B  10 NLPTYKLVVVGDGGVGKSALTIQFFQKIFVDEYDPTIEDSYRKHTEIDNQWAILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTRDQGKEMATKYNIPYIETSAKDPPLNVDKTFHDLVRVIRQQ 178
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         


Chain P from PDB  Type:PROTEIN  Length:168
 aligned with RASM_MOUSE | O08989 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:168
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
           RASM_MOUSE    11 LPTYKLVVVGDGGVGKSALTIQFFQKIFVPDYDPTIEDSYLKHTEIDNQWAILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTRDQGKEMATKYNIPYIETSAKDPPLNVDKTFHDLVRVIRQQ 178
               SCOP domains d3kkop_ P: automated matches                                                                                                                                             SCOP domains
               CATH domains 3kkoP00 P:11-178 P-loop containing nucleotide triphosphate hydrolases                                                                                                    CATH domains
           Pfam domains (1) ----Ras-3kkoP01 P:15-177                                                                                                                                               - Pfam domains (1)
           Pfam domains (2) ----Ras-3kkoP02 P:15-177                                                                                                                                               - Pfam domains (2)
           Pfam domains (3) ----Ras-3kkoP03 P:15-177                                                                                                                                               - Pfam domains (3)
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhh...eee........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kko P  11 LPTYKLVVVGDGGVGKSALTIQFFQKIFVDEYDPTIEDSYRKHTEIDNQWAILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTRDQGKEMATKYNIPYIETSAKDPPLNVDKTFHDLVRVIRQQ 178
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: Ras (176)
(-)
Mus musculus (Mouse) (16)
1aRas-3kkoP01P:15-177
1bRas-3kkoP02P:15-177
1cRas-3kkoP03P:15-177

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,P   (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: 1x1r 1x1s 3kkp 3kkq 3pir 3pit

(-) Related Entries Specified in the PDB File

1x1r 1x1s 3kkm 3kkn 3kkp 3kkq