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(-) Description

Title :  SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S4 DELTA 41, REFINED WITH DIPOLAR COUPLINGS (ENSEMBLE OF 16 STRUCTURES)
 
Authors :  M. A. Markus, R. B. Gerstner, D. E. Draper, D. A. Torchia
Date :  14 Jul 99  (Deposition) - 29 Sep 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (16x)
Keywords :  Two Subdomains, Unique Topology, Possible Helix-Turn Helix Motif, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Markus, R. B. Gerstner, D. E. Draper, D. A. Torchia
Refining The Overall Structure And Subdomain Orientation Of Ribosomal Protein S4 Delta41 With Dipolar Couplings Measured By Nmr In Uniaxial Liquid Crystalline Phases.
J. Mol. Biol. V. 292 375 1999
PubMed-ID: 10493882  |  Reference-DOI: 10.1006/JMBI.1999.3061
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN S4 DELTA 41
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET13A
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentS4 DELTA 41 (S4 RESIDUES 42-200)
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422

 Structural Features

(-) Chains, Units

  
NMR Structure (16x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1C06)

(-) Sites  (0, 0)

(no "Site" information available for 1C06)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C06)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1C06)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C06)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_S4PS00632 Ribosomal protein S4 signature.RS4_GEOSE90-114  1A:49-73
2S4PS50889 S4 RNA-binding domain profile.RS4_GEOSE92-152  1A:51-111

(-) Exons   (0, 0)

(no "Exon" information available for 1C06)

(-) Sequences/Alignments

NMR Structure
   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:159
 aligned with RS4_GEOSE | P81288 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:159
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191         
            RS4_GEOSE    42 RKLSEYGLQLQEKQKLRHMYGVNERQFRKTFEEAGKMPGKHGENFMILLESRLDNLVYRLGLARTRRQARQLVTHGHIIVDGSRVNIPSYRVKPGQTIAVREKSRNLQVIKEALEANNYIPDYLSFDPEKMEGTYTRLPERSELPAEINEALIVEFYSR 200
               SCOP domains d1c06a_ A: Ribosomal protein S4                                                                                                                                 SCOP domains
               CATH domains 1c06A01 A:1-51,A:140-159                           1c06A02 A:52-139                                                                        1c06A01              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..eee..ee............eeee......hhhhhhhhhh.......eeee....eeee..............hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------RIBOSOMAL_S4  PDB: A:49-7-------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------S4  PDB: A:51-111 UniProt: 92-152                            ------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c06 A   1 MKLSEYGLQLQEKQKLRHMYGVNERQFRKTFEEAGKMPGKHGENFMILLESRLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQTIAVREKSRNLQVIKEALEANNYIPDYLSFDPEKMEGTYTRLPERSELPAEINEALIVEFYSR 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (2, 2)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C06)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (RS4_GEOSE | P81288)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0046677    response to antibiotic    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 antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
    GO:0015935    small ribosomal subunit    The smaller of the two subunits of a ribosome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RS4_GEOSE | P812881c05 1eg0 1qd7

(-) Related Entries Specified in the PDB File

1c05 MINIMIZED AVERAGE STRUCTURE