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(-) Description

Title :  CRYSTAL STRUCTURE OF RND3/RHOE: FUNCTIONAL IMPLICATIONS
 
Authors :  D. Fiegen, L. Blumenstein, P. Stege, I. R. Vetter, M. R. Ahmadian
Date :  19 Jul 02  (Deposition) - 07 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Small Gtpase, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Fiegen, L. Blumenstein, P. Stege, I. R. Vetter, M. R. Ahmadian
Crystal Structure Of Rnd3/Rhoe: Functional Implications
Febs Lett. V. 525 100 2002
PubMed-ID: 12163169  |  Reference-DOI: 10.1016/S0014-5793(02)03094-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RND3/RHOE SMALL GTP-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX4T1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RND3(RESIDUES 19-200)
    Gene: RND3 (AMINO ACIDS 19-200)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RHO-RELATED GTP-BINDING PROTEIN RHOE

 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
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:37 , THR A:55 , GTP A:538 , HOH A:1000 , HOH A:1041BINDING SITE FOR RESIDUE MG A 550
2AC2SOFTWARESER A:32 , GLN A:33 , CYS A:34 , GLY A:35 , LYS A:36 , THR A:37 , ALA A:38 , PHE A:48 , TYR A:52 , THR A:55 , GLY A:80 , TYR A:83 , LYS A:136 , ASP A:138 , LEU A:139 , SER A:178 , ALA A:179 , LEU A:180 , MG A:550 , HOH A:1000 , HOH A:1003 , HOH A:1009 , HOH A:1012 , HOH A:1041 , HOH A:1045 , HOH A:1046BINDING SITE FOR RESIDUE GTP A 538

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M7B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M7B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M7B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M7B)

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3cENST000003757343cENSE00001513357chr2:151344181-151343782400RND3_HUMAN1-50501A:22-5029
1.5bENST000003757345bENSE00000777716chr2:151343295-15134320888RND3_HUMAN51-80301A:51-8030
1.7cENST000003757347cENSE00002146645chr2:151331498-151331389110RND3_HUMAN80-116371A:80-11637
1.8cENST000003757348cENSE00001661670chr2:151328275-151328141135RND3_HUMAN117-161451A:117-16145
1.9eENST000003757349eENSE00001070099chr2:151326752-1513247092044RND3_HUMAN162-244831A:162-20039

(-) 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:179
 aligned with RND3_HUMAN | P61587 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:179
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191         
           RND3_HUMAN    22 VKCKIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDLRTDVSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSENSVRDIFHVATLACVNK 200
               SCOP domains d1m7ba_ A: RhoE (RND3)                                                                                                                                                              SCOP domains
               CATH domains 1m7bA00 A:22-200 P-loop containing nucleotide triphosphate hydrolases                                                                                                               CATH domains
               Pfam domains ---Ras-1m7bA01 A:25-199                                                                                                                                                           - Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh..........eeeeeeeee....eeeeeeeee..hhhhh.hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3c  PDB: A:22-50      Exon 1.5b  PDB: A:51-80       ------------------------------------Exon 1.8c  PDB: A:117-161 UniProt: 117-161   Exon 1.9e  PDB: A:162-200 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.7c  PDB: A:80-116             ------------------------------------------------------------------------------------ Transcript 1 (2)
                 1m7b A  22 VKCKIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDLRTDVSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSENSVRDIFHVATLACVNK 200
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
   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  (1, 1)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RND3_HUMAN | P61587)
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: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: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:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    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: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RND3_HUMAN | P61587: 2v55 4bg6

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