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(-) Description

Title :  STRUCTURE OF THE PHACTR1 RPEL DOMAIN AND RPEL MOTIF DIRECTED ASSEMBLIES WITH G-ACTIN REVEAL THE MOLECULAR BASIS FOR ACTIN BINDING COOPERATIVITY.
 
Authors :  S. Mouilleron, M. Wiezlak, N. O'Reilly, R. Treisman, N. Q. Mcdonald
Date :  12 Jul 12  (Deposition) - 31 Jul 13  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  B,M
Keywords :  Structural Protein, Nucleotide-Binding, Transcription Regulation, Muscle Protein, Atp-Binding, Cytoskeleton (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Mouilleron, M. Wiezlak, N. O'Reilly, R. Treisman, N. Q. Mcdonald
Structures Of The Phactr1 Rpel Domain And Rpel Motif Complexes With G-Actin Reveal The Molecular Basis For Actin Binding Cooperativity.
Structure V. 20 1960 2012
PubMed-ID: 23041370  |  Reference-DOI: 10.1016/J.STR.2012.08.031

(-) Compounds

Molecule 1 - ACTIN, ALPHA SKELETAL MUSCLE
    ChainsB
    Organism CommonRABBIT
    Organism ScientificORYCTOLAGUS CUNICULUS
    Organism Taxid9986
    SynonymALPHA-ACTIN-1
    TissueMUSCLE
 
Molecule 2 - PHOSPHATASE AND ACTIN REGULATOR 1
    ChainsM
    Organism CommonRABBIT
    Organism ScientificORYCTOLAGUS CUNICULUS
    Organism Taxid9986
    SynonymPHOSPHATASE AND ACTIN REGULATOR 1, ISOFORM CRA_C
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit BM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 5)

Asymmetric/Biological Unit (5, 5)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CA1Ligand/IonCALCIUM ION
3LAB1Ligand/IonLATRUNCULIN B
4MG1Ligand/IonMAGNESIUM ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:15 , LEU B:16 , PRO B:32 , ILE B:34 , GLN B:59 , TYR B:69 , ASP B:157 , GLY B:182 , ARG B:183 , THR B:186 , ARG B:206 , GLU B:207 , ARG B:210 , ATP B:1377 , HOH B:2103BINDING SITE FOR RESIDUE LAB B1376
2AC2SOFTWAREGLY B:13 , SER B:14 , GLY B:15 , LEU B:16 , LYS B:18 , GLY B:156 , ASP B:157 , GLY B:158 , VAL B:159 , GLY B:182 , ARG B:210 , LYS B:213 , GLU B:214 , GLY B:301 , GLY B:302 , THR B:303 , MET B:305 , TYR B:306 , LYS B:336 , LAB B:1376 , MG B:1378 , HOH B:2004 , HOH B:2005 , HOH B:2013 , HOH B:2061 , HOH B:2077 , HOH B:2100 , HOH B:2101 , HOH B:2147 , HOH B:2148BINDING SITE FOR RESIDUE ATP B1377
3AC3SOFTWAREATP B:1377 , HOH B:2002 , HOH B:2004 , HOH B:2061 , HOH B:2148BINDING SITE FOR RESIDUE MG B1378
4AC4SOFTWAREHIS B:73 , ASP B:179 , HOH B:2086BINDING SITE FOR RESIDUE TRS B1379
5AC5SOFTWAREPHE M:133 , LYS M:134 , HIS M:135 , THR M:136BINDING SITE FOR RESIDUE CA M1163

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B1U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B1U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B1U)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACTINS_1PS00406 Actins signature 1.ACTS_MOUSE55-65  1B:53-63
2ACTINS_ACT_LIKEPS01132 Actins and actin-related proteins signature.ACTS_MOUSE106-118  1B:104-116
3RPELPS51073 RPEL repeat profile.PHAR1_MOUSE138-163
422-447
460-485
498-523
  1M:138-162
-
-
-
4ACTINS_2PS00432 Actins signature 2.ACTS_MOUSE358-366  1B:356-364

(-) Exons   (0, 0)

(no "Exon" information available for 4B1U)

(-) 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 B from PDB  Type:PROTEIN  Length:349
 aligned with ACTS_MOUSE | P68134 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:371
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376 
           ACTS_MOUSE     7 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF 377
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeee.......eeee....---------------..hhhhhhhh.........ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhh.-------.eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhhhh...eehhhhhhhh.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b1u B   5 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVG---------------SYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMAT-------EKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF 375
                                    14        24        34 |       -       |54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    |    -  |    244       254       264       274       284       294       304       314       324       334       344       354       364       374 
                                                          36              52                                                                                                                                                                              229     237                                                                                                                                          

Chain M from PDB  Type:PROTEIN  Length:30
 aligned with PHAR1_MOUSE | Q2M3X8 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:30
                                   142       152       162
          PHAR1_MOUSE   133 FKHTSAALERKISMRQSREELIKRGVLKEI 162
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh..hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE -----RPEL  PDB: M:138-162      PROSITE
                 Transcript ------------------------------ Transcript
                 4b1u M 133 FKHTSAALERKISMRQSREELIKRGVLKEI 162
                                   142       152       162

   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 4B1U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B1U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B1U)

(-) Gene Ontology  (40, 41)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (ACTS_MOUSE | P68134)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0090131    mesenchyme migration    The process in which the population of cells that make up a mesenchyme undergo directed movement.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0009991    response to extracellular stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus.
    GO:0010226    response to lithium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lithium (Li+) ion stimulus.
    GO:0009612    response to mechanical stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0048545    response to steroid hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus.
    GO:0043503    skeletal muscle fiber adaptation    Any process in which the skeletal muscle fibers change their phenotypic profiles in response to altered functional demands and a variety of signals. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
    GO:0048741    skeletal muscle fiber development    The process whose specific outcome is the progression of the skeletal muscle fiber over time, from its formation to the mature structure. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
    GO:0030240    skeletal muscle thin filament assembly    The aggregation, arrangement and bonding together of proteins to form the actin-based thin filaments of myofibrils in skeletal muscle.
cellular component
    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:0005884    actin filament    A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    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: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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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: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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0030017    sarcomere    The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
    GO:0001725    stress fiber    A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.
    GO:0005865    striated muscle thin filament    Filaments formed of actin and associated proteins; attached to Z discs at either end of sarcomeres in myofibrils.

Chain M   (PHAR1_MOUSE | Q2M3X8)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0008157    protein phosphatase 1 binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 1.
    GO:0004864    protein phosphatase inhibitor activity    Stops, prevents or reduces the activity of a protein phosphatase, an enzyme that hydrolyzes phosphate groups from phosphorylated proteins.
biological process
    GO:0031532    actin cytoskeleton reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0031032    actomyosin structure 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 containing both actin and myosin or paramyosin. The myosin may be organized into filaments.
    GO:0048870    cell motility    Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
    GO:0043149    stress fiber assembly    The aggregation, arrangement and bonding together of a set of components to form a stress fiber. A stress fiber is a contractile actin filament bundle that consists of short actin filaments with alternating polarity.
cellular component
    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: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: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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        ACTS_MOUSE | P681341alm 1atn 1h1v 1t44 1uy5
        PHAR1_MOUSE | Q2M3X84b1v 4b1w 4b1x 4b1y 4b1z

(-) Related Entries Specified in the PDB File

4b1v STRUCTURE OF THE PHACTR1 RPEL-N DOMAIN BOUND TO G- ACTIN
4b1w STRUCTURE OF THE PHACTR1 RPEL-2 DOMAIN BOUND TO ACTIN
4b1x STRUCTURE OF THE PHACTR1 RPEL-2 BOUND TO G-ACTIN
4b1y STRUCTURE OF THE PHACTR1 RPEL-3 BOUND TO G-ACTIN
4b1z STRUCTURE OF THE PHACTR1 RPEL DOMAIN BOUND TO G- ACTIN