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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN RHOC-GDP COMPLEX
 
Authors :  S. M. G. Dias, R. A. Cerione
Date :  14 Mar 06  (Deposition) - 27 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Gtp-Binding Protein, Gtpase, Signaling Protein, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. G. Dias, R. A. Cerione
X-Ray Crystal Structures Reveal Two Activated States For Rhoc.
Biochemistry V. 46 6547 2007
PubMed-ID: 17497936  |  Reference-DOI: 10.1021/BI700035P

(-) Compounds

Molecule 1 - RHO-RELATED GTP-BINDING PROTEIN RHOC
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21 (DE3) RP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RHOC, ARH9, ARHC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: H9

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:19 , THR A:37 , GDP A:1001 , HOH A:3143 , HOH A:3144 , HOH A:3145BINDING SITE FOR RESIDUE MG A 2001
2AC2SOFTWAREALA A:15 , CYS A:16 , GLY A:17 , LYS A:18 , THR A:19 , CYS A:20 , PHE A:30 , VAL A:35 , LYS A:118 , ASP A:120 , LEU A:121 , SER A:160 , ALA A:161 , LYS A:162 , MG A:2001 , HOH A:3011 , HOH A:3046 , HOH A:3049 , HOH A:3059 , HOH A:3079 , HOH A:3143 , HOH A:3144 , HOH A:3145 , HOH A:3197BINDING SITE FOR RESIDUE GDP A 1001
3AC3SOFTWAREPHE A:154 , THR A:163 , GLU A:165 , HOH A:3073BINDING SITE FOR RESIDUE EDO A 3001
4AC4SOFTWAREARG A:122 , ALA A:177 , GLY A:178 , LEU A:179 , EDO A:3003 , HOH A:3102 , HOH A:3117 , HOH A:3118 , HOH A:3125BINDING SITE FOR RESIDUE EDO A 3002
5AC5SOFTWAREARG A:176 , LEU A:179 , EDO A:3002 , HOH A:3051 , HOH A:3179BINDING SITE FOR RESIDUE EDO A 3003
6AC6SOFTWAREGLY A:62 , ASP A:67 , ARG A:70 , LYS A:98 , TRP A:99 , HOH A:3044 , HOH A:3122 , HOH A:3163 , HOH A:3188BINDING SITE FOR RESIDUE EDO A 3004
7AC7SOFTWAREILE A:43 , ASP A:45 , ASP A:90BINDING SITE FOR RESIDUE EDO A 3005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GCN)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051974D120HRHOC_HUMANPolymorphism11538959AD120H
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003696421aENSE00001450517chr1:113250056-113249700357RHOC_HUMAN-00--
1.4aENST000003696424aENSE00002194010chr1:113246428-113246266163RHOC_HUMAN1-52521A:3-5250
1.6bENST000003696426bENSE00001020610chr1:113245741-113245621121RHOC_HUMAN53-93411A:53-9341
1.6gENST000003696426gENSE00001683192chr1:113245315-113245185131RHOC_HUMAN93-136441A:93-13644
1.7kENST000003696427kENSE00001896032chr1:113244335-113243753583RHOC_HUMAN137-193571A:137-17943

(-) 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:177
 aligned with RHOC_HUMAN | P08134 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       
           RHOC_HUMAN     3 AIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYIADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRQDEHTRRELAKMKQEPVRSEEGRDMANRISAFGYLECSAKTKEGVREVFEMATRAGL 179
               SCOP domains d2gcna_ A: RhoC                                                                                                                                                                   SCOP domains
               CATH domains 2gcnA00 A:3-179 P-loop containing nucleotide triphosphate hydrolases                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh..............eeeeee..eeeeeeee......hhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhh......hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------H----------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: A:3-52 UniProt: 1-52 [INCOMPLETE] Exon 1.6b  PDB: A:53-93 UniProt: 53-93   -------------------------------------------Exon 1.7k  PDB: A:137-179 UniProt: 137-193  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------Exon 1.6g  PDB: A:93-136 UniProt: 93-136    ------------------------------------------- Transcript 1 (2)
                 2gcn A   3 AIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYIADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRQDEHTRRELAKMKQEPVRSEEGRDMANRISAFGYLECSAKTKEGVREVFEMATRAGL 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GCN)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RHOC_HUMAN | P08134)
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: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:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0043297    apical junction assembly    The formation of an apical junction, a functional unit located near the cell apex at the points of contact between epithelial cells composed of the tight junction, the zonula adherens junction and the desmosomes, by the aggregation, arrangement and bonding together of its constituents.
    GO:0000910    cytokinesis    The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0060193    positive regulation of lipase activity    Any process that increases the frequency, rate or extent of lipase activity, the hydrolysis of a lipid or phospholipid.
    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:1902766    skeletal muscle satellite cell migration    The orderly movement of a skeletal muscle satellite cell from one site to another. Migration of these cells is a key step in the process of growth and repair of skeletal muscle cells.
    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:0044319    wound healing, spreading of cells    The migration of a cell along or through a wound gap that contributes to the reestablishment of a continuous surface.
cellular component
    GO:0032154    cleavage furrow    The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
    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: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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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
        RHOC_HUMAN | P08134: 1z2c 2gco 2gcp

(-) Related Entries Specified in the PDB File

2gco CRYSTAL STRUCTURE OF THE HUMAN RHOC-GPPNHP COMPLEX
2gcp CRYSTAL STRUCTURE OF THE HUMAN RHOC-GSP COMPLEX