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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN T217V TTHL1 IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS
 
Authors :  A. G. Gabdulkhakov, N. A. Nevskaya, S. V. Nikonov
Date :  11 Oct 11  (Deposition) - 31 Oct 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Ribosomal Protein, Rrna, Ribosome, L1 Protuberance In The Ribosome, Rna-Rna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. V. Tishchenko, E. Y. Nikonova, O. S. Kostareva, A. G. Gabdulkhakov, A. V. Sarskikh, W. Piendl, S. V. Nikonov, M. B. Garber, N. A. Nevskaya
Crystal Structure Of Ribosomal Protein Tthl1 In Complex Wit 80Nt 23S Rna From Thermus Thermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 50S RIBOSOMAL PROTEIN L1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A-PL/TTHL1 T217V
    Expression System StrainBL11(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneRPLA, RPL1
    MutationYES
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid274
 
Molecule 2 - RNA (80-MER)
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC18/RRNATTH
    Expression System StrainBL11(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid274
    Other DetailsFRAGMENT OF 23S RRNA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1MG11Ligand/IonMAGNESIUM ION
2MLI1Ligand/IonMALONATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:215 , THR A:216 , GLY A:219 , HOH A:404 , C B:2175 , A B:2176BINDING SITE FOR RESIDUE MG A 301
02AC2SOFTWAREU B:2109 , G B:2110 , G B:2120 , C B:2178 , HOH B:2336 , HOH B:2339BINDING SITE FOR RESIDUE MLI B 2201
03AC3SOFTWAREMG B:2203 , HOH B:2307 , HOH B:2308 , HOH B:2309 , HOH B:2310 , HOH B:2311 , HOH B:2313BINDING SITE FOR RESIDUE MG B 2202
04AC4SOFTWAREG B:2110 , C B:2111 , MG B:2202 , HOH B:2310 , HOH B:2312 , HOH B:2313 , HOH B:2314 , HOH B:2316BINDING SITE FOR RESIDUE MG B 2203
05AC5SOFTWAREG B:2156 , MG B:2206 , HOH B:2351 , HOH B:2352 , HOH B:2353 , HOH B:2371BINDING SITE FOR RESIDUE MG B 2204
06AC6SOFTWAREALA A:33 , C B:2138 , C B:2139 , HOH B:2358 , HOH B:2359 , HOH B:2360BINDING SITE FOR RESIDUE MG B 2205
07AC7SOFTWAREHOH A:426 , G B:2156 , G B:2157 , MG B:2204 , MG B:2209 , HOH B:2371 , HOH B:2372 , HOH B:2373BINDING SITE FOR RESIDUE MG B 2206
08AC8SOFTWAREU B:2122 , G B:2123 , HOH B:2375 , HOH B:2381 , HOH B:2382BINDING SITE FOR RESIDUE MG B 2207
09AC9SOFTWAREG B:2125 , HOH B:2376 , HOH B:2383 , HOH B:2394 , HOH B:2395BINDING SITE FOR RESIDUE MG B 2208
10BC1SOFTWAREGLU A:202 , HOH A:426 , G B:2157 , MG B:2206 , HOH B:2372 , HOH B:2385 , HOH B:2386 , HOH B:2387BINDING SITE FOR RESIDUE MG B 2209
11BC2SOFTWAREG B:2149 , U B:2150 , HOH B:2326 , HOH B:2342 , HOH B:2378BINDING SITE FOR RESIDUE MG B 2210
12BC3SOFTWAREU B:2150 , G B:2151 , HOH B:2318 , HOH B:2326 , HOH B:2341BINDING SITE FOR RESIDUE MG B 2211

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U56)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U56)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U56)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L1PS01199 Ribosomal protein L1 signature.RL1_THETH121-140  1A:120-139

(-) Exons   (0, 0)

(no "Exon" information available for 3U56)

(-) 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:228
 aligned with RL1_THETH | P27150 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:228
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
           RL1_THETH      2 PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS  229
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh........hhhhhhhhhhhh.......eeeeeeee.....hhhhh.eeeee..........eeee...hhhhhhhhhh..eeehhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh...............hhhhhhhhhhh.eeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhh..........eeeeeeee....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L1        ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3u56 A    1 PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTVMGPSVRINPHS  228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        

Chain B from PDB  Type:RNA  Length:80
                                                                                                                 
                3u56 B 2105 GGGAUGCGUAGGAUAGGUGGGAGCCUGUGAACCCCCGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUUCCC 2184
                                  2114      2124      2134      2144      2154      2164      2174      2184

   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 3U56)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U56)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U56)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RL1_THETH | P27150)
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.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    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:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0015934    large ribosomal subunit    The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        RL1_THETH | P271501ad2 1eg0 1zho 2hw8 2oum 2ov7 2vpl 3tg8 3u4m 3umy 487d 4f9t 4qg3 4qgb 4qvi 4reo 5ib7 5ib8 5ibb 5imq 5imr 5j8b

(-) Related Entries Specified in the PDB File

1mzp STRUCTURE OF THE L1 PROTUBERANCE IN THE RIBOSOME
1u63 THE STRUCTURE OF A RIBOSOMAL PROTEIN L1-MRNA COMPLEX
1zho THE STRUCTURE OF A RIBOSOMAL PROTEIN L1 IN COMPLEX WITH MRNA
2hw8 STRUCTURE OF RIBOSOMAL PROTEIN L1-MRNA COMPLEX AT 2.1 RESOLUTION
2vpl THE STRUCTURE OF THE COMPLEX BETWEEN THE FIRST DOMAIN OF L1 PROTEIN FROM THERMUS THERMOPHILUS AND MRNA FROM METHANOCOCCUS JANNASCHII
3u42
3u4m CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN TTHL1 IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS