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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RHOGAP DOMAIN OF RICS
 
Authors :  L. Nedyalkova, W. Tempel, Y. Tong, Y. Li, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  31 Aug 09  (Deposition) - 29 Sep 09  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics Consortium (Sgc), Gap, Alternative Splicing, Cell Junction, Cell Membrane, Cell Projection, Cytoplasm, Endoplasmic Reticulum, Endosome, Golgi Apparatus, Gtpase Activation, Membrane, Phosphoprotein, Postsynaptic Cell Membrane, Sh3 Domain, Synapse (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Nedyalkova, W. Tempel, Y. Tong, Y. Li, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Rhogap Domain Of Rics
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHO/CDC42/RAC GTPASE-ACTIVATING PROTEIN RICS
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-V2R-PRARE2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRHO-GAP DOMAIN: UNP RESIDUES 367-577
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymP200RHOGAP, P250GAP, RHOGAP INVOLVED IN THE BETA- CATENIN-N-CADHERIN AND NMDA RECEPTOR SIGNALING, BRAIN- SPECIFIC RHO GTPASE-ACTIVATING PROTEIN, GAB-ASSOCIATED CDC42/RAC GTPASE-ACTIVATING PROTEIN, GC-GAP, GTPASE REGULATOR INTERACTING WITH TRKA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1UNX11Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1UNX2Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1UNX9Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 3IUG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:433 -Pro A:434
2Glu B:433 -Pro B:434

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHOGAPPS50238 Rho GTPase-activating proteins domain profile.RHG32_HUMAN372-567
 
  2A:372-567
B:372-567
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHOGAPPS50238 Rho GTPase-activating proteins domain profile.RHG32_HUMAN372-567
 
  1A:372-567
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHOGAPPS50238 Rho GTPase-activating proteins domain profile.RHG32_HUMAN372-567
 
  1-
B:372-567

(-) Exons   (0, 0)

(no "Exon" information available for 3IUG)

(-) 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:184
 aligned with RHG32_HUMAN | A7KAX9 from UniProtKB/Swiss-Prot  Length:2087

    Alignment length:203
                                   375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565   
          RHG32_HUMAN   366 KERVFGCDLGEHLLNSGFEVPQVLQSCTAFIERYGIVDGIYRLSGVASNIQRLRHEFDSEHVPDLTKEPYVQDIHSVGSLCKLYFRELPNPLLTYQLYEKFSDAVSAATDEERLIKIHDVIQQLPPPHYRTLEFLMRHLSLLADYCSITNMHAKNLAIVWAPNLLRSKQIESACFSGTAAFMEVRIQSVVVEFILNHVDVLFS 568
               SCOP domains d3iuga_ A: automated matches                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh...hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh........hhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..-------------------hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------RHOGAP  PDB: A:372-567 UniProt: 372-567                                                                                                                                                             - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iug A 366 GERVFGCDLGEHLLNSGFEVPQVLQSCTAFIERYGIVDGIYRLSGVASNIQRLRHEFDSEHVPDLTKEPYVQDIHSVGSLCKLYFRELPNPLLTYQLYEKFSDAVSAATDEERLIKIHDVIQQLPPPHYRTLEFLMRHLSLLADYCSITNMHAKNLAIVWAPNLLRS-------------------QSVVVEFILNHVDVLFS 568
                                   375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525      |  -         -      |555       565   
                                                                                                                                                                                                532                 552                

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with RHG32_HUMAN | A7KAX9 from UniProtKB/Swiss-Prot  Length:2087

    Alignment length:202
                                   377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567  
          RHG32_HUMAN   368 RVFGCDLGEHLLNSGFEVPQVLQSCTAFIERYGIVDGIYRLSGVASNIQRLRHEFDSEHVPDLTKEPYVQDIHSVGSLCKLYFRELPNPLLTYQLYEKFSDAVSAATDEERLIKIHDVIQQLPPPHYRTLEFLMRHLSLLADYCSITNMHAKNLAIVWAPNLLRSKQIESACFSGTAAFMEVRIQSVVVEFILNHVDVLFSG 569
               SCOP domains d3iugb_ B: automated matches                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh...hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh........hhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..----------------hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RHOGAP  PDB: B:372-567 UniProt: 372-567                                                                                                                                                             -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iug B 368 RVFGCDLGEHLLNSGFEVPQVLQSCTAFIERYGIVDGIYRLSGVASNIQRLRHEFDSEHVPDLTKEPYVQDIHSVGSLCKLYFRELPNPLLTYQLYEKFSDAVSAATDEERLIKIHDVIQQLPPPHYRTLEFLMRHLSLLADYCSITNMHAKNLAIVWAPNLLRS----------------VRIQSVVVEFILNHVDVLFSG 569
                                   377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527    |    -         - |     557       567  
                                                                                                                                                                                              532              549                    

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IUG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IUG)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RHG32_HUMAN | A7KAX9)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    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: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.
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:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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