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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH A TRNA ACCEPTOR STEM MIMIC (ASM) AND THE ANTIBIOTIC SPARSOMYCIN
 
Authors :  A. Bashan, I. Agmon, R. Zarivatch, F. Schluenzen, J. M. Harms, R. Berisio, H. Bartels, H. A. Hansen, A. Yonath
Date :  02 Jan 03  (Deposition) - 11 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym./Biol. Unit :  K,T,0,5
Keywords :  Ribosomes, Trna, Puromycin, Sparsomycin, Peptidyl- Transferase, Peptide Bond Formation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bashan, I. Agmon, R. Zarivatch, F. Schluenzen, J. M. Harms, R. Berisio, H. Bartels, F. Franceschi, T. Auerbach, H. A. Hansen, E. Kossoy, M. Kessler, A. Yonath
Structural Basis Of The Ribosomal Machinery For Peptide Bond Formation, Translocation, And Nascent Chain Progression
Mol. Cell V. 11 91 2003
PubMed-ID: 12535524  |  Reference-DOI: 10.1016/S1097-2765(03)00009-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 23S RIBOSOMAL RNA
    Chains: 0
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
 
Molecule 2 - TRNA ACCEPTOR STEM MIMIC
    Chains: 5
    Engineered: YES
    Other Details: THE TERMINAL C OF ASM WAS COUPLED VIA A PHOSPHODIESTER BOND TO THE 5 OH OF THE N6-DIMETHYL MOIETY OF PUROMYCIN
    Synthetic: YES
 
Molecule 3 - 50S RIBOSOMAL PROTEIN L16
    Chains: K
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
 
Molecule 4 - GENERAL STRESS PROTEIN CTC
    Chains: T
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : KT05

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1PPU1Mod. NucleotidePUROMYCIN-5'-MONOPHOSPHATE
2SPS1Ligand/IonSPARSOMYCIN

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA 0:2581BINDING SITE FOR RESIDUE SPS 0 2881

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L16_1PS00586 Ribosomal protein L16 signature 1.RL16_DEIRA59-70  1K:60-71
2RIBOSOMAL_L16_2PS00701 Ribosomal protein L16 signature 2.RL16_DEIRA82-93  1K:83-94

(-) Exons   (0, 0)

(no "Exon" information available for 1NJM)

(-) 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
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Chain 0 from PDB  Type:RNA  Length:2766
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                1njm 0    1 GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGAUUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGGGGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUCAGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAUCAGCCCAAAUUCAACCCCUCAAGCCGAAGUGGCUGGAAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGAGCGGUUGACUGUAAGGUCGUUGUUCGUGAAACGAUGACUGAAUCCGCGCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACUUACAAGCAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAGACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCGGAGCGAAAGCGAGUCCGAAUAGGGCGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCAGGUUGAAACCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUUGUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUUGAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUCACAAGGCUAAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCUGCGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUAAAUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAAUGAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUGGUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAAGUGCGGAUGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACAAGGGUUCCUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAACGGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGGACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAUCGGGUCAGAAAAUCUACCGGUCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGAAGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUACCGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUUAAGGAACUUUGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGGGGCGCAGUGAAUAGGCCCAGGCGACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAACAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAAGCUGCGAAAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCAACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGAAAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGUGGGAGAAACUGGCCGGUCGGUGGCCACCCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUAGUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGACGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACACGUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAGAGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGUAGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUGAGUUCUCCCACUGUUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGCGUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCA 2877
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                                                                                                                                                                                                                                                                                 248|                                                                              373|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     891|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              2097|   2110|    2125|    2140|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     2774|                                                                                                   
                                                                                                                                                                                                                                                                                  292                                                                               387                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      911                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               2103    2117     2132     2157                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      2778                                                                                                   


Chain 5 from PDB  Type:RNA  Length:25
                                                          
                1njm 5    1 GGGGCUAAGCCGCUUAGCUCCACCa   35
                                    10|       30    |
                                    10|            35-PPU
                                     21              


Chain K from PDB  Type:PROTEIN  Length:124
 aligned with RL16_DEIRA | Q9RXJ5 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:124
                                    16        26        36        46        56        66        76        86        96       106       116       126    
          RL16_DEIRA      7 TKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHKLPIQTK  130
               SCOP domains d1njmk_ K: 50S subunit                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------RIBOSOMAL_L1-----------RIBOSOMAL_L1------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                1njm K    8 TKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHKLPIQTK  131
                                    17        27        37        47        57        67        77        87        97       107       117       127    


Chain T from PDB  Type:PROTEIN  Length:223
 aligned with RL25_DEIRA | Q9RX88 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
          RL25_DEIRA      1 MELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPRLTAEELEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASE  223
               SCOP domains d1njmt_ T: 50S subunit                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1njm T    1 MELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPRLTAEELEAEVQAAQVAGLVAAGELSEEAAEAVLEGDASLEEVKAEASE  223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Low resolution protein structures (283)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1NJM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain K   (RL16_DEIRA | Q9RXJ5)
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: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: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.

Chain T   (RL25_DEIRA | Q9RX88)
molecular function
    GO:0008097    5S rRNA binding    Interacting selectively and non-covalently with 5S ribosomal RNA, the smallest RNA constituent of a ribosome.
    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: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: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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  1njm
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  RL25_DEIRA | Q9RX88
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 Related Entries

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

UniProtKB/Swiss-Prot
        RL16_DEIRA | Q9RXJ5: 1gs2 1njp 1nkw 1nwx 1nwy 1sm1 1xbp 1y69 2zjp 2zjq 2zjr 3cf5 3dll 3pio 3pip 4io9 4ioa 4ioc 4u67 4v49 4v4a 4v4g 4wfn 5dm6 5dm7 5jvg 5jvh
        RL25_DEIRA | Q9RX88: 1njp 1nkw 1nwx 1nwy 1sm1 1xbp 2zjp 2zjq 2zjr 3cf5 3dll 3pio 3pip 4io9 4ioa 4ioc 4u67 4v49 4v4a 4v4g 4v4p 4v4r 4v4s 4v4t 4wfn 5dm6 5dm7 5jvg 5jvh

(-) Related Entries Specified in the PDB File

1jzx COMPLEX OF DEINOCOCCUS RADIODURANS 50S WITH CLINDAMYCIN
1jzy COMPLEX OF DEINOCOCCUS RADIODURANS 50S WITH ERYTHROMYCIN
1jzz COMPLEX OF DEINOCOCCUS RADIODURANS 50S WITH ROXITHROMYCIN
1k00 COMPLEX OF DEINOCOCCUS RADIODURANS 50S WITH CLARITHROMYCIN
1k01 COMPLEX OF DEINOCOCCUS RADIODURANS 50S WITH CHLORAMPHENICOL
1njn COMPLEX OF DEINOCOCCUS RADIODURANS 50S WITH SPARSOMYCIN
1njo COMPLEX OF DEINOCOCCUS RADIODURANS 50S WITH ACCP
1njp COMPLEX OF DEINOCOCCUS RADIODURANS 50S WITH ASM
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