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(-) Description

Title :  THE CRYSTAL STRUCTURE OF RHOUA IN THE GDP-BOUND STATE.
 
Authors :  C. Gileadi, X. Yang, E. Papagrigoriou, J. Elkins, Y. Zhao, J. Bray, O. Gi C. Umeano, E. Ugochukwu, J. Uppenberg, G. Bunkoczi, F. Von Delft, A. C C. Phillips, P. Savitsky, O. Fedorov, A. Edwards, J. Weigelt, C. H. Arr M. Sundstrom, D. A. Doyle, Structural Genomics Consortium (Sgc)
Date :  30 May 07  (Deposition) - 19 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A
Keywords :  Gtpase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Gileadi, X. Yang, E. Papagrigoriou, J. Elkins, Y. Zhao, J. Bray, O. Gileadi, C. Umeano, E. Ugochukwu, J. Uppenberg, G. Bunkoczi, F. Von Delft, A. C. W. Pike, C. Phillips, P. Savitsky, O. Fedorov, A. Edwards, J. Weigelt, C. H. Arrowsmith, M. Sundstrom, D. A. Doyle
The Crystal Structure Of Rhoua In The Gdp-Bound State.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RAS HOMOLOG GENE FAMILY, MEMBER U
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3) WITH WITH PRARE PLASMID ENCODING RARE CODON TRNAS,(CHLORAMPHENICOL-RESISTANT)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRHOU
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAS-LIKE GENE FAMILY MEMBER U, WRCH-1, RYU GTPASE, CDC42- LIKE GTPASE, RHO GTPASE-LIKE PROTEIN ARHU, GTP-BINDING PROTEIN LIKE 1

 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
1AC1SOFTWARETHR A:63 , GDP A:3444 , HOH A:3499 , HOH A:3500 , HOH A:3501 , HOH A:3504BINDING SITE FOR RESIDUE MG A 1
2AC2SOFTWAREMG A:1 , ALA A:59 , VAL A:60 , GLY A:61 , LYS A:62 , THR A:63 , SER A:64 , GLN A:162 , ASP A:164 , LEU A:165 , SER A:204 , ALA A:205 , LEU A:206 , HOH A:3450 , HOH A:3454 , HOH A:3465 , HOH A:3466 , HOH A:3482 , HOH A:3499 , HOH A:3500 , HOH A:3501 , HOH A:3533BINDING SITE FOR RESIDUE GDP A 3444

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:149 -A:178

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q3H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051975T121ARHOU_HUMANPolymorphism3820264AT121A

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q3H)

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003666911ENSE00001442330chr1:228870824-228871751928RHOU_HUMAN1-88881A:49-88 (gaps)40
1.2ENST000003666912ENSE00000792996chr1:228873420-22887347859RHOU_HUMAN88-107201A:88-10720
1.3aENST000003666913aENSE00001442329chr1:228879032-2288824163385RHOU_HUMAN108-2581511A:108-227120

(-) 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:171
 aligned with RHOU_HUMAN | Q7L0Q8 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:179
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218         
           RHOU_HUMAN    49 GVKCVLVGDGAVGKTSLVVSYTTNGYPTEYIPTAFDNFSAVVSVDGRPVRLQLCDTAGQDEFDKLRPLCYTNTDIFLLCFSVVSPSSFQNVSEKWVPEIRCHCPKAPIILVGTQSDLREDVKVLIELDKCKEKPVPEEAAKLCAEEIKAASYIECSALTQKNLKEVFDAAIVAGIQYSD 227
               SCOP domains d2q3ha_ A: automated ma        tches                                                                                                                                                SCOP domains
               CATH domains 2q3hA00 A:49-227 P-loop         containing nucleotide triphosphate hydrolases                                                                                                       CATH domains
               Pfam domains --Ras-2q3hA01 A:51-224                                                                                                                                                          --- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhh--------....eeeeeeeee..eeeeeeeee.........hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------A---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:49-88 (gaps)           -------------------Exon 1.3a  PDB: A:108-227 UniProt: 108-258 [INCOMPLETE]                                                                  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.2            ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2q3h A  49 GVKCVLVGDGAVGKTSLVVSYTT--------PTAFDNFSAVVSVDGRPVRLQLCDTAGQDEFDKLRPLCYTNTDIFLLCFSVVSPSSFQNVSEKWVPEIRCHCPKAPIILVGTQSDLREDVKVLIELDKCKEKPVPEEAAKLLAEEIKAASYIECSALTQKNLKEVFDAAIVAGIQYSD 227
                                    58        68  |      - |      88        98       108       118       128       138       148       158       168       178       188       198       208       218         
                                                 71       80                                                                                                                                                   

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Family: Ras (176)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RHOU_HUMAN | Q7L0Q8)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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).
biological process
    GO:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0016601    Rac protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Rac family of proteins switching to a GTP-bound active state.
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
    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: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: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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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.
    GO:0002102    podosome    An actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell, contain an F-actin-rich core surrounded by a ring structure containing proteins such as vinculin and talin, and have a diameter of 0.5 mm.

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2q3h