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(-) Description

Title :  DETAILED VIEW OF A KEY ELEMENT OF THE RIBOSOME ASSEMBLY: CRYSTAL STRUCTURE OF THE S15-RRNA COMPLEX
 
Authors :  A. Nikulin, A. Serganov, E. Ennifar, S. Tischenko, N. Nevskaya
Date :  06 Dec 99  (Deposition) - 02 Apr 00  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribosome, S15, Protein, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Nikulin, A. Serganov, E. Ennifar, S. Tishchenko, N. Nevskaya, W. Shepard, C. Portier, M. Garber, B. Ehresmann, C. Ehresmann, S. Nikonov, P. Dumas
Crystal Structure Of The S15-Rrna Complex.
Nat. Struct. Biol. V. 7 273 2000
PubMed-ID: 10742169  |  Reference-DOI: 10.1038/74028

(-) Compounds

Molecule 1 - RRNA FRAGMENT
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
 
Molecule 2 - 30S RIBOSOMAL PROTEIN S15
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 2-87
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1K1Ligand/IonPOTASSIUM ION
2MG9Ligand/IonMAGNESIUM ION
3MSE4Mod. Amino AcidSELENOMETHIONINE
4NA2Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG B:26BINDING SITE FOR RESIDUE MG B 201
2AC2SOFTWAREC B:48 , G B:49BINDING SITE FOR RESIDUE MG B 202
3AC3SOFTWAREU B:39BINDING SITE FOR RESIDUE MG B 205
4AC4SOFTWAREU B:42BINDING SITE FOR RESIDUE MG B 208
5AC5SOFTWAREA B:52BINDING SITE FOR RESIDUE MG B 209
6AC6SOFTWAREHOH B:319BINDING SITE FOR RESIDUE NA B 210
7AC7SOFTWAREC B:4 , G B:54 , C B:55BINDING SITE FOR RESIDUE NA B 211
8AC8SOFTWAREHIS A:150BINDING SITE FOR RESIDUE K A 213

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DK1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DK1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DK1)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_S15PS00362 Ribosomal protein S15 signature.RS15_THETH39-69  1A:138-168

(-) Exons   (0, 0)

(no "Exon" information available for 1DK1)

(-) 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:86
 aligned with RS15_THETH | P80378 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:86
                                    11        21        31        41        51        61        71        81      
           RS15_THETH     2 PITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGI  87
               SCOP domains d1dk1a_ A: Ribosomal protein S15                                                       SCOP domains
               CATH domains 1dk1A00 A:101-186  [code=1.10.287.10, no name defined]                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------RIBOSOMAL_S15  PDB: A:138-168  ------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 1dk1 A 101 PITKEEKQKVmQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLmmVGQRRRLLRYLQREDPERYRmLIEKLGI 186
                                   110|      120       130       140       150      |160       170       180      
                                    111-MSE                                       157-MSE               179-MSE   
                                                                                   158-MSE                        


Chain B from PDB  Type:RNA  Length:57
                                                                                         
                 1dk1 B   1 GGGCGGCCUUCGGGCUAGACGGUGGGAGAGGCUUCGGCUGGUCCACCCGUGACGCUC  57
                                    10        20        30        40        50
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DK1)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RS15_THETH | P80378)
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: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.

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  1dk1
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  RS15_THETH | P80378
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 Related Entries

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

UniProtKB/Swiss-Prot
        RS15_THETH | P80378: 1ab3 1eg0 1f7y 1fjg 1fka 1hnw 1hnx 1hnz 1hr0 1i94 1i95 1i96 1i97 1ibk 1ibl 1ibm 1j5e 1kuq 1l1u 1n32 1n33 1twt 1xmo 1xmq 1xnq 1xnr 2f4v 2fkx 2hhh 3oto 4aqy 4v49 4v8x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1DK1)