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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIMERIC REGULATORY DOMAIN OF MOUSE DIAPHANEOUS-RELATED FORMIN (DRF), MDIA1
 
Authors :  T. Otomo, C. Otomo, D. R. Tomchick, M. Machius, M. K. Rosen
Date :  05 Apr 05  (Deposition) - 13 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Autoinhibition, Actin, Nucleation, Cytoskeleton, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Otomo, C. Otomo, D. R. Tomchick, M. Machius, M. K. Rosen
Structural Basis Of Rho Gtpase-Mediated Activation Of The Formin Mdia1
Mol. Cell V. 18 273 2005
PubMed-ID: 15866170  |  Reference-DOI: 10.1016/J.MOLCEL.2005.04.002

(-) Compounds

Molecule 1 - DIAPHANOUS PROTEIN HOMOLOG 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET
    Expression System Vector TypePLASMID
    FragmentAMINO-TERMINAL DOMAIN, RESIDUES 131-516
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymDIAPHANOUS-RELATED FORMIN 1, DRF1, MDIA1, P140MDIA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (0, 0)

(no "Site" information available for 2BNX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:262 -Pro A:263
2Gln B:262 -Pro B:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BNX)

(-) 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:338
 aligned with DIAP1_MOUSE | O08808 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:343
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472   
          DIAP1_MOUSE   133 SRSAMMYIQELRSGLRDMHLLSCLESLRVSLNNNPVSWVQTFGAEGLASLLDILKRLHDEKEETSGNYDSRNQHEIIRCLKAFMNNKFGIKTMLETEEGILLLVRAMDPAVPNMMIDAAKLLSALCILPQPEDMNERVLEAMTERAEMDEVERFQPLLDGLKSGTSIALKVGCLQLINALITPAEELDFRVHIRSELMRLGLHQVLQELREIENEDMKVQLCVFDEQGDEDFFDLKGRLDDIRMEMDDFGEVFQIILNTVKDSKAEPHFLSILQHLLLVRNDYEARPQYYKLIEECVSQIVLHKNGTDPDFKCRHLQIDIERLVDQMIDKTKVEKSEAKATEL 475
               SCOP domains d2bnxa1 A:133-475 Diaphanous protein homolog 1, Diap1 (Dia1, DRF1)                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...hhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.................-----.hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bnx A 133 SRSAMMYIQELRSGLRDMHLLSCLESLRVSLNNNPVSWVQTFGAEGLASLLDILKRLHDEKEETSGNYDSRNQHEIIRCLKAFMNNKFGIKTMLETEEGILLLVRAMDPAVPNMMIDAAKLLSALCILPQPEDMNERVLEAMTERAEMDEVERFQPLLDGLKSGTSIALKVGCLQLINALITPAEELDFRVHIRSELMRLGLHQVLQELREIENEDMKVQLCVFDEQGDEDFFDLKGRLDDIRMEMDDFGEVFQIILNTVKDSKAEPHFLSILQHLLLVRNDYEARPQYYKLIEECVSQIVLHKNGTDPDFKCRHLQIDIERLV-----KTKVEKSEAKATEL 475
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452   |   462       472   
                                                                                                                                                                                                                                                                                                                                                             456   462             

Chain B from PDB  Type:PROTEIN  Length:339
 aligned with DIAP1_MOUSE | O08808 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:342
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472  
          DIAP1_MOUSE   133 SRSAMMYIQELRSGLRDMHLLSCLESLRVSLNNNPVSWVQTFGAEGLASLLDILKRLHDEKEETSGNYDSRNQHEIIRCLKAFMNNKFGIKTMLETEEGILLLVRAMDPAVPNMMIDAAKLLSALCILPQPEDMNERVLEAMTERAEMDEVERFQPLLDGLKSGTSIALKVGCLQLINALITPAEELDFRVHIRSELMRLGLHQVLQELREIENEDMKVQLCVFDEQGDEDFFDLKGRLDDIRMEMDDFGEVFQIILNTVKDSKAEPHFLSILQHLLLVRNDYEARPQYYKLIEECVSQIVLHKNGTDPDFKCRHLQIDIERLVDQMIDKTKVEKSEAKATE 474
               SCOP domains d2bnxb_ B: Diaphanous protein homolog 1, Diap1 (Dia1, DRF1)                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh---....hhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bnx B 133 SRSAMMYIQELRSGLRDMHLLSCLESLRVSLNNNPVSWVQTFGAEGLASLLDILKRLHDEKEETSGNYDSRNQHEIIRCLKAFMNNKFGIKTMLETEEGILLLVRAMDPAVPNMMIDAAKLLSALCILPQPEDMNERVLEAMTERAEMDEVERFQPLLDGLKSGTSIALKVGCLQLINALITPAEELDFRVHIRSELMRLGLHQVLQELREIENEDMKVQLCVFDEQGDEDFFDLKGRLD---MEMDDFGEVFQIILNTVKDSKAEPHFLSILQHLLLVRNDYEARPQYYKLIEECVSQIVLHKNGTDPDFKCRHLQIDIERLVDQMIDKTKVEKSEAKATE 474
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372   |   382       392       402       412       422       432       442       452       462       472  
                                                                                                                                                                                                                                                                         372 376                                                                                                  

   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/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DIAP1_MOUSE | O08808)
molecular function
    GO:0017048    Rho GTPase binding    Interacting selectively and non-covalently with Rho protein, any member of the Rho subfamily of the Ras superfamily of monomeric GTPases. Proteins in the Rho subfamily are involved in relaying signals from cell-surface receptors to the actin cytoskeleton.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0005522    profilin binding    Interacting selectively and non-covalently with profilin, an actin-binding protein that forms a complex with G-actin and prevents it from polymerizing to form F-actin.
    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: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:0030041    actin filament polymerization    Assembly of actin filaments by the addition of actin monomers to a filament.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0016043    cellular component organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
    GO:0071420    cellular response to histamine    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a histamine stimulus. Histamine, the biogenic amine 2-(1H-imidazol-4-yl)ethanamine, is involved in local immune responses as well as regulating physiological function in the gut and acting as a neurotransmitter.
    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:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0035372    protein localization to microtubule    A process in which a protein is transported to, or maintained at, a microtubule.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0032886    regulation of microtubule-based process    Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton.
    GO:0051279    regulation of release of sequestered calcium ion into cytosol    Any process that modulates the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
cellular component
    GO:0005903    brush border    The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
    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:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0072686    mitotic spindle    A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DIAP1_MOUSE | O088081v9d 1z2c 2bap 2f31 2v8f 3eg5 3o4x 3obv 4uwx

(-) Related Entries Specified in the PDB File

1v9d CRYSTAL STRUCTURE OF THE CORE FH2 DOMAIN OF MOUSE MDIA1