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(-) Description

Title :  RIBOSOMAL PROTEIN L10-L12(NTD) COMPLEX, SPACE GROUP P21
 
Authors :  M. Diaconu, U. Kothe, F. Schluenzen, N. Fischer, J. M. Harms, A. G. Tonevitski, H. Stark, M. V. Rodnina, M. C. Wahl
Date :  07 Apr 05  (Deposition) - 12 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,U,V,W,X,Y,Z
Keywords :  Ribosome Structure And Function, L10-L12 Complex Structure, L10E Structure, L7/12 Ribosomal Stalk, Thiostrepton Loop Of 23S Rrna, Translation Factor Recruitment, Gtpase Stimulation, Mechanism Of Translation, X-Ray Crystallography, Rapid Kinetics, Cryo-Electron Microscopy, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Diaconu, U. Kothe, F. Schluenzen, N. Fischer, J. M. Harms, A. G. Tonevitski, H. Stark, M. V. Rodnina, M. C. Wahl
Structural Basis For The Function Of The Ribosomal L7/12 Stalk In Factor Binding And Gtpase Activation.
Cell(Cambridge, Mass. ) V. 121 991 2005
PubMed-ID: 15989950  |  Reference-DOI: 10.1016/J.CELL.2005.04.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 50S RIBOSOMAL PROTEIN L10
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM-ZZ
    Expression System Strain: DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RPLJ
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
 
Molecule 2 - 50S RIBOSOMAL PROTEIN L7/L12
    Chains: U, V, W, X, Y, Z
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Gene: RPLL
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit : AUVWXYZ

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1ZAV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L10PS01109 Ribosomal protein L10 signature.RL10_THEMA7-41  1A:7-41

(-) Exons   (0, 0)

(no "Exon" information available for 1ZAV)

(-) 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:178
 aligned with RL10_THEMA | P29394 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:178
                             1                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169        
           RL10_THEMA     - -MLTRQQKELIVKEMSEIFKKTSLILFADFLGFTVADLTELRSRLREKYGDGARFRVVKNTLLNLALKNAEYEGYEEFLKGPTAVLYVTEGDPVEAVKIIYNFYKDKKADLSRLKGGFLEGKKFTAEEVENIAKLPSKEELYAMLVGRVKAPITGLVFALSGILRNLVYVLNAIKEKK 177
               SCOP domains -d1zava1 A:1-177 Ribosomal protein L10                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Ribosomal_L10-1zavA01 A:2-104                                                                          ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhh....hhhhh...eeeeee....hhhhhhhhhhhhhhh..hhh.eeeeee..eeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------RIBOSOMAL_L10  PDB: A:7-41         ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zav A   0 VMLTRQQKELIVKEMSEIFKKTSLILFADFLGFTVADLTELRSRLREKYGDGARFRVVKNTLLNLALKNAEYEGYEEFLKGPTAVLYVTEGDPVEAVKIIYNFYKDKKADLSRLKGGFLEGKKFTAEEVENIAKLPSKEELYAMLVGRVKAPITGLVFALSGILRNLVYVLNAIKEKK 177
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169        


Chain U from PDB  Type:PROTEIN  Length:30
 aligned with RL7_THEMA | P29396 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:30
                                    10        20        30
            RL7_THEMA     1 MTIDEIIEAIEKLTVSELAELVKKLEDKFG  30
               SCOP domains d1zavu1 U:1-30                 SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 1zav U   1 MTIDEIIEAIEKLTVSELAELVKKLEDKFG  30
                                    10        20        30


Chain V from PDB  Type:PROTEIN  Length:30
 aligned with RL7_THEMA | P29396 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:30
                                    10        20        30
            RL7_THEMA     1 MTIDEIIEAIEKLTVSELAELVKKLEDKFG  30
               SCOP domains d1zavv1 V:1-30                 SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 1zav V   1 MTIDEIIEAIEKLTVSELAELVKKLEDKFG  30
                                    10        20        30


Chain W from PDB  Type:PROTEIN  Length:30
 aligned with RL7_THEMA | P29396 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:30
                                    10        20        30
            RL7_THEMA     1 MTIDEIIEAIEKLTVSELAELVKKLEDKFG  30
               SCOP domains d1zavw1 W:1-30                 SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 1zav W   1 MTIDEIIEAIEKLTVSELAELVKKLEDKFG  30
                                    10        20        30


Chain X from PDB  Type:PROTEIN  Length:29
 aligned with RL7_THEMA | P29396 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:29
                                    10        20         
            RL7_THEMA     1 MTIDEIIEAIEKLTVSELAELVKKLEDKF  29
               SCOP domains d1zavx1 X:1-29                SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
                 Transcript ----------------------------- Transcript
                 1zav X   1 MTIDEIIEAIEKLTVSELAELVKKLEDKF  29
                                    10        20         


Chain Y from PDB  Type:PROTEIN  Length:29
 aligned with RL7_THEMA | P29396 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:29
                                    10        20         
            RL7_THEMA     1 MTIDEIIEAIEKLTVSELAELVKKLEDKF  29
               SCOP domains d1zavy1 Y:1-29                SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
                 Transcript ----------------------------- Transcript
                 1zav Y   1 MTIDEIIEAIEKLTVSELAELVKKLEDKF  29
                                    10        20         


Chain Z from PDB  Type:PROTEIN  Length:27
 aligned with RL7_THEMA | P29396 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:27
                                    11        21       
            RL7_THEMA     2 TIDEIIEAIEKLTVSELAELVKKLEDK  28
               SCOP domains d1zavz1 Z:2-28              SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                 1zav Z   2 TIDEIIEAIEKLTVSELAELVKKLEDK  28
                                    11        21
   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  (2, 7)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Ribosomal_L10] (3)

(-) Gene Ontology  (10, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RL10_THEMA | P29394)
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: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: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 U,V,W,X,Y,Z   (RL7_THEMA | P29396)
molecular function
    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: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.

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  1zav
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 Related Entries

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

UniProtKB/Swiss-Prot
        RL10_THEMA | P29394: 1zaw 1zax
        RL7_THEMA | P29396: 1dd3 1dd4 1l1u 1zaw 1zax

(-) Related Entries Specified in the PDB File

1zaw 1zax 1zb4