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  • Articles  (72)
  • Models, Molecular  (72)
  • 2020-2023
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  • Articles  (72)
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  • 1
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    Functional mimicry of a protein hormone by a peptide agonist: the EPO receptor complex at 2.8 A (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-26
    Description: The functional mimicry of a protein by an unrelated small molecule has been a formidable challenge. Now, however, the biological activity of a 166-residue hematopoietic growth hormone, erythropoietin (EPO), with its class 1 cytokine receptor has been mimicked by a 20-residue cyclic peptide unrelated in sequence to the natural ligand. The crystal structure at 2.8 A resolution of a complex of this agonist peptide with the extracellular domain of EPO receptor reveals that a peptide dimer induces an almost perfect twofold dimerization of the receptor. The dimer assembly differs from that of the human growth hormone (hGH) receptor complex and suggests that more than one mode of dimerization may be able to induce signal transduction and cell proliferation. The EPO receptor binding site, defined by peptide interaction, corresponds to the smaller functional epitope identified for hGH receptor. Similarly, the EPO mimetic peptide ligand can be considered as a minimal hormone, and suggests the design of nonpeptidic small molecule mimetics for EPO and other cytokines may indeed be achievable.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Livnah, O -- Stura, E A -- Johnson, D L -- Middleton, S A -- Mulcahy, L S -- Wrighton, N C -- Dower, W J -- Jolliffe, L K -- Wilson, I A -- GM-49497/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 26;273(5274):464-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10666 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662530" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Drug Design ; Erythropoietin/*chemistry/*metabolism ; Growth Hormone/chemistry/metabolism ; Humans ; Hydrogen Bonding ; Models, Molecular ; *Molecular Mimicry ; Molecular Sequence Data ; Peptides, Cyclic/*chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Erythropoietin/*agonists/chemistry/metabolism ; Receptors, Somatotropin/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-21
    Description: The T cell receptor (TCR) inherently has dual specificity. T cells must recognize self-antigens in the thymus during maturation and then discriminate between foreign pathogens in the periphery. A molecular basis for this cross-reactivity is elucidated by the crystal structure of the alloreactive 2C TCR bound to self peptide-major histocompatibility complex (pMHC) antigen H-2Kb-dEV8 refined against anisotropic 3.0 angstrom resolution x-ray data. The interface between peptide and TCR exhibits extremely poor shape complementarity, and the TCR beta chain complementarity-determining region 3 (CDR3) has minimal interaction with the dEV8 peptide. Large conformational changes in three of the TCR CDR loops are induced upon binding, providing a mechanism of structural plasticity to accommodate a variety of different peptide antigens. Extensive TCR interaction with the pMHC alpha helices suggests a generalized orientation that is mediated by the Valpha domain of the TCR and rationalizes how TCRs can effectively "scan" different peptides bound within a large, low-affinity MHC structural framework for those that provide the slight additional kinetic stabilization required for signaling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia, K C -- Degano, M -- Pease, L R -- Huang, M -- Peterson, P A -- Teyton, L -- Wilson, I A -- AI42266/AI/NIAID NIH HHS/ -- AI42267/AI/NIAID NIH HHS/ -- R01 CA58896/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1998 Feb 20;279(5354):1166-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9469799" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallization ; Crystallography, X-Ray ; H-2 Antigens/*chemistry/*immunology/metabolism ; Ligands ; Mice ; Mice, Transgenic ; Models, Molecular ; Mutation ; Oligopeptides/*chemistry/immunology/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/*immunology/metabolism ; Recombinant Proteins
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Crystallographic evidence for preformed dimers of erythropoietin receptor before ligand activation (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-02-12
    Description: Erythropoietin receptor (EPOR) is thought to be activated by ligand-induced homodimerization. However, structures of agonist and antagonist peptide complexes of EPOR, as well as an EPO-EPOR complex, have shown that the actual dimer configuration is critical for the biological response and signal efficiency. The crystal structure of the extracellular domain of EPOR in its unliganded form at 2.4 angstrom resolution has revealed a dimer in which the individual membrane-spanning and intracellular domains would be too far apart to permit phosphorylation by JAK2. This unliganded EPOR dimer is formed from self-association of the same key binding site residues that interact with EPO-mimetic peptide and EPO ligands. This model for a preformed dimer on the cell surface provides insights into the organization, activation, and plasticity of recognition of hematopoietic cell surface receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Livnah, O -- Stura, E A -- Middleton, S A -- Johnson, D L -- Jolliffe, L K -- Wilson, I A -- GM49497/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Feb 12;283(5404):987-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9974392" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/chemistry ; Crystallography, X-Ray ; Dimerization ; Erythropoietin/metabolism ; Humans ; Hydrogen Bonding ; Janus Kinase 2 ; Ligands ; Models, Molecular ; Peptide Fragments/*chemistry/metabolism ; Peptides, Cyclic/metabolism ; Protein Conformation ; Protein-Tyrosine Kinases/metabolism ; *Proto-Oncogene Proteins ; Receptors, Erythropoietin/*chemistry/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    The crystal structure of a T cell receptor in complex with peptide and MHC class II (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-03
    Description: The crystal structure of a complex involving the D10 T cell receptor (TCR), 16-residue foreign peptide antigen, and the I-Ak self major histocompatibility complex (MHC) class II molecule is reported at 3.2 angstrom resolution. The D10 TCR is oriented in an orthogonal mode relative to its peptide-MHC (pMHC) ligand, necessitated by the amino-terminal extension of peptide residues projecting from the MHC class II antigen-binding groove as part of a mini beta sheet. Consequently, the disposition of D10 complementarity-determining region loops is altered relative to that of most pMHCI-specific TCRs; the latter TCRs assume a diagonal orientation, although with substantial variability. Peptide recognition, which involves P-1 to P8 residues, is dominated by the Valpha domain, which also binds to the class II MHC beta1 helix. That docking is limited to one segment of MHC-bound peptide offers an explanation for epitope recognition and altered peptide ligand effects, suggests a structural basis for alloreactivity, and illustrates how bacterial superantigens can span the TCR-pMHCII surface.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reinherz, E L -- Tan, K -- Tang, L -- Kern, P -- Liu, J -- Xiong, Y -- Hussey, R E -- Smolyar, A -- Hare, B -- Zhang, R -- Joachimiak, A -- Chang, H C -- Wagner, G -- Wang, J -- AI/CA37581/AI/NIAID NIH HHS/ -- AI19807/AI/NIAID NIH HHS/ -- GM56008/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Dec 3;286(5446):1913-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Immunobiology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10583947" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens/*chemistry/immunology/metabolism ; Binding Sites ; CD4-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/immunology ; Conalbumin/chemistry/immunology ; Crystallization ; Crystallography, X-Ray ; Histocompatibility Antigens Class I/immunology ; Histocompatibility Antigens Class II/*chemistry/immunology/metabolism ; Hydrogen Bonding ; Ligands ; Mice ; Mice, Inbred AKR ; Models, Molecular ; Oligopeptides/chemistry/immunology/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology/metabolism ; Superantigens/immunology/metabolism ; Thymus Gland/cytology/immunology
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  • 5
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    Domain movement in gelsolin: a calcium-activated switch (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-03
    Description: The actin-binding protein gelsolin is involved in remodeling the actin cytoskeleton during growth-factor signaling, apoptosis, cytokinesis, and cell movement. Calcium-activated gelsolin severs and caps actin filaments. The 3.4 angstrom x-ray structure of the carboxyl-terminal half of gelsolin (G4-G6) in complex with actin reveals the basis for gelsolin activation. Calcium binding induces a conformational rearrangement in which domain G6 is flipped over and translated by about 40 angstroms relative to G4 and G5. The structural reorganization tears apart the continuous beta sheet core of G4 and G6. This exposes the actin-binding site on G4, enabling severing and capping of actin filaments to proceed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Robinson, R C -- Mejillano, M -- Le, V P -- Burtnick, L D -- Yin, H L -- Choe, S -- New York, N.Y. -- Science. 1999 Dec 3;286(5446):1939-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Laboratory, Salk Institute for Biological Studies, Post Office Box 85800, San Diego, CA 92186-5800, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10583954" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Gelsolin/*chemistry/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 6
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    Crystal structure of the cytochrome bc1 complex from bovine heart mitochondria (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-07-04
    Description: On the basis of x-ray diffraction data to a resolution of 2.9 angstroms, atomic models of most protein components of the bovine cytochrome bc1 complex were built, including core 1, core 2, cytochrome b, subunit 6, subunit 7, a carboxyl-terminal fragment of cytochrome c1, and an amino-terminal fragment of the iron-sulfur protein. The positions of the four iron centers within the bc1 complex and the binding sites of the two specific respiratory inhibitors antimycin A and myxothiazol were identified. The membrane-spanning region of each bc1 complex monomer consists of 13 transmembrane helices, eight of which belong to cytochrome b. Closely interacting monomers are arranged as symmetric dimers and form cavities through which the inhibitor binding pockets can be accessed. The proteins core 1 and core 2 are structurally similar to each other and consist of two domains of roughly equal size and identical folding topology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xia, D -- Yu, C A -- Kim, H -- Xia, J Z -- Kachurin, A M -- Zhang, L -- Yu, L -- Deisenhofer, J -- GM 30721/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jul 4;277(5322):60-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9204897" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antimycin A/metabolism/pharmacology ; Binding Sites ; Cattle ; Crystallography, X-Ray ; Cytochrome b Group/chemistry ; Cytochromes c1/chemistry ; Dimerization ; Electron Transport Complex III/*chemistry/metabolism ; Intracellular Membranes/enzymology ; Iron/metabolism ; Methacrylates ; Mitochondria, Heart/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thiazoles/metabolism/pharmacology
    Print ISSN: 0036-8075
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  • 7
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    Hormone-dependent coactivator binding to a hydrophobic cleft on nuclear receptors (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-06-20
    Description: The ligand-binding domain of nuclear receptors contains a transcriptional activation function (AF-2) that mediates hormone-dependent binding of coactivator proteins. Scanning surface mutagenesis on the human thyroid hormone receptor was performed to define the site that binds the coactivators, glucocorticoid receptor-interacting protein 1 (GRIP1) and steroid receptor coactivator 1 (SRC-1). The residues involved encircle a small surface that contains a hydrophobic cleft. Ligand activation of transcription involves formation of this surface by folding the carboxyl-terminal alpha helix against a scaffold of three other helices. These features may represent general ones for nuclear receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feng, W -- Ribeiro, R C -- Wagner, R L -- Nguyen, H -- Apriletti, J W -- Fletterick, R J -- Baxter, J D -- Kushner, P J -- West, B L -- DK09516/DK/NIDDK NIH HHS/ -- DK51281/DK/NIDDK NIH HHS/ -- P41-RR01081/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1998 Jun 12;280(5370):1747-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Metabolic Research Unit, Box 0540, University of California San Francisco, San Francisco, CA 94143-0540, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9624051" target="_blank"〉PubMed〈/a〉
    Keywords: HeLa Cells ; Histone Acetyltransferases ; Humans ; Ligands ; Models, Molecular ; Mutagenesis, Site-Directed ; Nuclear Receptor Coactivator 1 ; Nuclear Receptor Coactivator 2 ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Retinoic Acid/metabolism ; Receptors, Thyroid Hormone/*chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Retinoid X Receptors ; Transcription Factors/*metabolism ; *Transcriptional Activation ; Triiodothyronine/*metabolism/pharmacology
    Print ISSN: 0036-8075
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  • 8
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    Molecular basis for interactions of G protein betagamma subunits with effectors (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-06-20
    Description: Both the alpha and betagamma subunits of heterotrimeric guanine nucleotide-binding proteins (G proteins) communicate signals from receptors to effectors. Gbetagamma subunits can regulate a diverse array of effectors, including ion channels and enzymes. Galpha subunits bound to guanine diphosphate (Galpha-GDP) inhibit signal transduction through Gbetagamma subunits, suggesting a common interface on Gbetagamma subunits for Galpha binding and effector interaction. The molecular basis for interaction of Gbetagamma with effectors was characterized by mutational analysis of Gbeta residues that make contact with Galpha-GDP. Analysis of the ability of these mutants to regulate the activity of calcium and potassium channels, adenylyl cyclase 2, phospholipase C-beta2, and beta-adrenergic receptor kinase revealed the Gbeta residues required for activation of each effector and provides evidence for partially overlapping domains on Gbeta for regulation of these effectors. This organization of interaction regions on Gbeta for different effectors and Galpha explains why subunit dissociation is crucial for signal transmission through Gbetagamma subunits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ford, C E -- Skiba, N P -- Bae, H -- Daaka, Y -- Reuveny, E -- Shekter, L R -- Rosal, R -- Weng, G -- Yang, C S -- Iyengar, R -- Miller, R J -- Jan, L Y -- Lefkowitz, R J -- Hamm, H E -- DA02121/DA/NIDA NIH HHS/ -- DA02575/DA/NIDA NIH HHS/ -- MH40165/MH/NIMH NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1998 May 22;280(5367):1271-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Neuroscience and Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, IL 60611, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9596582" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate Ribose/metabolism ; Adenylyl Cyclases/metabolism ; Binding Sites ; Calcium Channels/metabolism ; Cell Line ; Cyclic AMP-Dependent Protein Kinases/metabolism ; G Protein-Coupled Inwardly-Rectifying Potassium Channels ; GTP-Binding Proteins/*chemistry/*metabolism ; Guanosine Diphosphate/metabolism ; *Heterotrimeric GTP-Binding Proteins ; Humans ; Isoenzymes/metabolism ; Models, Molecular ; Mutation ; Phospholipase C beta ; Potassium Channels/metabolism ; *Potassium Channels, Inwardly Rectifying ; Protein Conformation ; Rhodopsin/pharmacology ; *Signal Transduction ; Transducin/metabolism ; Type C Phospholipases/metabolism ; beta-Adrenergic Receptor Kinases
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  • 9
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    Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-09-13
    Description: The solution structure of a human immunodeficiency virus type-1 (HIV-1) Rev peptide bound to stem-loop IIB of the Rev response element (RRE) RNA was solved by nuclear magnetic resonance spectroscopy. The Rev peptide has an alpha-helical conformation and binds in the major groove of the RNA near a purine-rich internal loop. Several arginine side chains make base-specific contacts, and an asparagine residue contacts a G.A base pair. The phosphate backbone adjacent to a G.G base pair adopts an unusual structure that allows the peptide to access a widened major groove. The structure formed by the two purine-purine base pairs of the RRE creates a distinctive binding pocket that the peptide can use for specific recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Battiste, J L -- Mao, H -- Rao, N S -- Tan, R -- Muhandiram, D R -- Kay, L E -- Frankel, A D -- Williamson, J R -- GM-08344/GM/NIGMS NIH HHS/ -- GM-39589/GM/NIGMS NIH HHS/ -- GM-53320/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Sep 13;273(5281):1547-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8703216" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/chemistry ; Asparagine/chemistry ; Base Composition ; Base Sequence ; *DNA-Binding Proteins ; Fungal Proteins/chemistry ; Gene Products, rev/*chemistry/*metabolism ; *Genes, env ; HIV-1/*chemistry ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Protein Kinases/chemistry ; *Protein Structure, Secondary ; RNA, Viral/*chemistry/genetics/metabolism ; *Saccharomyces cerevisiae Proteins ; Threonine/chemistry ; rev Gene Products, Human Immunodeficiency Virus
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  • 10
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    Crystal structure of the T4 regA translational regulator protein at 1.9 A resolution (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-05-26
    Description: The translational regulator protein regA is encoded by the T4 bacteriophage and binds to a region of messenger RNA (mRNA) that includes the initiator codon. RegA is unusual in that it represses the translation of about 35 early T4 mRNAs but does not affect nearly 200 other mRNAs. The crystal structure of regA was determined at 1.9 A resolution; the protein was shown to have an alpha-helical core and two regions with antiparallel beta sheets. One of these beta sheets has four antiparallel strands and has some sequence homology to RNP-1 and RNP-2, which are believed to be RNA-binding motifs and are found in a number of known RNA-binding proteins. Structurally guided mutants may help to uncover the basis for this variety of RNA interaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, C -- Chan, R -- Berger, I -- Lockshin, C -- Green, L -- Gold, L -- Rich, A -- New York, N.Y. -- Science. 1995 May 26;268(5214):1170-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7761833" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteriophage T4/*chemistry ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; RNA-Binding Proteins/*chemistry ; Structure-Activity Relationship ; Viral Proteins/*chemistry
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