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(-) Description

Title :  RUN DOMAIN OF RAP2 INTERACTING PROTEIN X, CRYSTALLIZED IN P2(1)2(1)2(1) SPACE GROUP
 
Authors :  M. Kukimoto-Niino, K. Murayama, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  11 Aug 06  (Deposition) - 24 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.22
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Run Domain, Effector, Rap2, Bundle, Protein Binding, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Kukimoto-Niino, T. Takagi, R. Akasaka, K. Murayama, T. Uchikubo-Kamo, T. Terada, M. Inoue, S. Watanabe, A. Tanaka, Y. Hayashizaki, T. Kigawa, M. Shirouzu, S. Yokoyama
Crystal Structure Of The Run Domain Of The Rap2-Interacting Protein X
J. Biol. Chem. V. 281 31843 2006
PubMed-ID: 16928684  |  Reference-DOI: 10.1074/JBC.M604960200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN RUFY3
    ChainsA, B
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidPK011025-09
    Expression System Vector TypePLASMID
    FragmentRUN DOMAIN
    GeneRUFY3, D5BWG0860E, RIPX
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymRAP2-INTERACTING PROTEIN X, RIPX

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2DWG)

(-) Sites  (0, 0)

(no "Site" information available for 2DWG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DWG)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUNPS50826 RUN domain profile.RUFY3_MOUSE95-227
 
  2A:113-245
B:113-245
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUNPS50826 RUN domain profile.RUFY3_MOUSE95-227
 
  1A:113-245
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUNPS50826 RUN domain profile.RUFY3_MOUSE95-227
 
  1-
B:113-245

(-) Exons   (0, 0)

(no "Exon" information available for 2DWG)

(-) 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    
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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:158
 aligned with RUFY3_MOUSE | Q9D394 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:165
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224     
          RUFY3_MOUSE    65 MANERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEVNALMMEEEGAIIAGLLVGLNVIDANFCMKGEDL 229
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....-------...hhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------RUN  PDB: A:113-245 UniProt: 95-227                                                                                                  -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dwg A  83 MANERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKA-------NKSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEVNALMMEEEGAIIAGLLVGLNVIDANFCMKGEDL 247
                                    92       102       112       122       132   |     - |     152       162       172       182       192       202       212       222       232       242     
                                                                               136     144                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:158
 aligned with RUFY3_MOUSE | Q9D394 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:165
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224     
          RUFY3_MOUSE    65 MANERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEVNALMMEEEGAIIAGLLVGLNVIDANFCMKGEDL 229
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....-------...hhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------RUN  PDB: B:113-245 UniProt: 95-227                                                                                                  -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dwg B  83 MANERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKA-------NKSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEVNALMMEEEGAIIAGLLVGLNVIDANFCMKGEDL 247
                                    92       102       112       122       132   |     - |     152       162       172       182       192       202       212       222       232       242     
                                                                               136     144                                                                                                       

   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  (0, 0)

(no "SCOP Domain" information available for 2DWG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DWG)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RUFY3_MOUSE | Q9D394)
molecular function
    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:0007015    actin filament 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. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0050771    negative regulation of axonogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of axonogenesis.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0045773    positive regulation of axon extension    Any process that activates or increases the frequency, rate or extent of axon extension.
    GO:0050772    positive regulation of axonogenesis    Any process that activates or increases the frequency, rate or extent of axonogenesis.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0090316    positive regulation of intracellular protein transport    Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells.
    GO:0050770    regulation of axonogenesis    Any process that modulates the frequency, rate or extent of axonogenesis, the generation of an axon, the long process of a neuron.
    GO:2000114    regulation of establishment of cell polarity    Any process that modulates the frequency, rate or extent of establishment of cell polarity.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    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:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0071437    invadopodium    A cell projection that emerges from the ECM-facing surface of a cell, is enriched in actin and associated cytoskeletal proteins, and displays localized proteolytic activity toward the substrate.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork 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:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RUFY3_MOUSE | Q9D3942cxf 2cxl 2dwk

(-) Related Entries Specified in the PDB File

1wus THE SAME PROTEIN CRYSTALLIZED IN P6(4)22 SPACE GROUP
2cxf THE SAME PROTEIN CRYSTALLIZED IN C2 SPACE GROUP
2cxl THE SAME PROTEIN CRYSTALLIZED IN I422 SPACE GROUP RELATED ID: MMK001003772.6 RELATED DB: TARGETDB