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(-) Description

Title :  N-TERMINAL FRAGMENT OF RIBOSOMAL PROTEIN L10 FROM METHANOCOCCUS JANNASCHII
 
Authors :  O. Kravchenko, I. Mitroshin, A. D. Nikulin, W. Piendl, M. Garber, S. Nik
Date :  11 Sep 09  (Deposition) - 26 May 10  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ribosomal Protein, L10, Ribonucleoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Kravchenko, I. Mitroshin, S. Nikonov, W. Piendl, M. Garber
Structure Of A Two-Domain N-Terminal Fragment Of Ribosomal Protein L10 From Methanococcus Jannaschii Reveals A Specifi Piece Of The Archaeal Ribosomal Stalk
J. Mol. Biol. V. 399 214 2010
PubMed-ID: 20399793  |  Reference-DOI: 10.1016/J.JMB.2010.04.017

(-) Compounds

Molecule 1 - ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11C
    Expression System Strain: BL21(DE3)PUBS520
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL FRAGMENT, RESIDUES IN UNP 10-221
    Gene: RPLP0, MJ0509
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: L10E, RIBOSOMAL PROTEIN L10

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3JSY)

(-) Sites  (0, 0)

(no "Site" information available for 3JSY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JSY)

(-) Exons   (0, 0)

(no "Exon" information available for 3JSY)

(-) Sequences/Alignments

Asymmetric 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:213
 aligned with RL10_METJA | P54049 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:213
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   
           RL10_METJA     9 VAPWKIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRDKVKLRMSRNTLIIRALKEAAEELNNPKLAELANYVERGAAILVTDMNPFKLYKLLEENKSPAPVRGGQIAPCDIKVEKGSTGMPPGPFLGELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKPIKVGLNILAVYEDGIIYTPDVLKVDEEKLLADI 221
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee..hhhhhhhhhhhh.eee...........eee..ee......hhhhhhhhh...eeee..eeee...eeee......hhhhhhhhhhh....eee..eeeeeee..eeehhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jsy A   9 MAPWKIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRDKVKLRMSRNTLIIRALKEAAEELNNPKLAELANYVERGAAILVTDMNPFKLYKLLEENKSPAPVRGGQIAPCDIKVEKGSTGMPPGPFLGELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKPIKVGLNILAVYEDGIIYTPDVLKVDEEKLLADI 221
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with RL10_METJA | P54049 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:205
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208     
           RL10_METJA     9 VAPWKIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRDKVKLRMSRNTLIIRALKEAAEELNNPKLAELANYVERGAAILVTDMNPFKLYKLLEENKSPAPVRGGQIAPCDIKVEKGSTGMPPGPFLGELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKPIKVGLNILAVYEDGIIYTPDVLKVD 213
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh.eee...........eee..eeeee...hhhhhhhhh...eeee..eeee...eeee......hhhhhhhhhhh....eee..eeeeeee..eeehhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jsy B   9 MAPWKIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRDKVKLRMSRNTLIIRALKEAAEELNNPKLAELANYVERGAAILVTDMNPFKLYKLLEENKSPAPVRGGQIAPCDIKVEKGSTGMPPGPFLGELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKPIKVGLNILAVYEDGIIYTPDVLKVD 213
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 3JSY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RL10_METJA | P54049)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0070180    large ribosomal subunit rRNA binding    Interacting selectively and non-covalently with the large ribosomal subunit RNA (LSU rRNA), a constituent of the large ribosomal subunit. In S. cerevisiae, this is the 25S rRNA.
    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:0002181    cytoplasmic translation    The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
    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:0022625    cytosolic large ribosomal subunit    The large subunit of a ribosome located in the cytosol.
    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:0030687    preribosome, large subunit precursor    A preribosomal complex consisting of 27SA, 27SB, and/or 7S pre-rRNA, 5S rRNA, ribosomal proteins including late-associating large subunit proteins, and associated proteins; a precursor of the eukaryotic cytoplasmic large ribosomal subunit.
    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
        RL10_METJA | P54049: 5d6g 5d8h 5dar

(-) Related Entries Specified in the PDB File

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