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(-) Description

Title :  X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES
 
Authors :  J. H. Cate, M. M. Yusupov, G. Zh. Yusupova, T. N. Earnest, H. F. Noller
Date :  09 Sep 99  (Deposition) - 04 Oct 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  7.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Functional Models Of 70S Ribosome, Trna, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Cate, M. M. Yusupov, G. Z. Yusupova, T. N. Earnest, H. F. Noller
X-Ray Crystal Structures Of 70S Ribosome Functional Complexes.
Science V. 285 2095 1999
PubMed-ID: 10497122  |  Reference-DOI: 10.1126/SCIENCE.285.5436.2095
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P-SITE TRNA OF 70S RIBOSOME
    Chains: A
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - P-SITE CODON OF 70S RIBOSOME
    Chains: B
    Engineered: YES
    Other Details: SEQUENCE FROM T. THERMOPHILUS
    Synthetic: YES
 
Molecule 3 - A-SITE TRNA OF 70S RIBOSOME
    Chains: C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 4 - A-SITE CODON OF 70S RIBOSOME
    Chains: D
    Engineered: YES
    Other Details: SEQUENCE FROM T. THERMOPHILUS
    Synthetic: YES
 
Molecule 5 - E-SITE TRNA OF 70S RIBOSOME
    Chains: E
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
 
Molecule 6 - PENULTIMATE STEM OF 16S RRNA IN THE 70S RIBOSOME
    Chains: F
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
 
Molecule 7 - 900 STEM-LOOP OF 16S RRNA IN THE 70S RIBOSOME
    Chains: G
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit : ABCDEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (12, 33)

Asymmetric/Biological Unit (12, 33)
No.NameCountTypeFull Name
11MA1Mod. Nucleotide6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
21MG2Mod. Nucleotide1N-METHYLGUANOSINE-5'-MONOPHOSPHATE
32MG1Mod. Nucleotide2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
45MC4Mod. Nucleotide5-METHYLCYTIDINE-5'-MONOPHOSPHATE
55MU3Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
67MG1Mod. Nucleotide7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
7H2U6Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
8IR4Ligand/IonIRIDIUM ION
9M2G2Mod. NucleotideN2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
10OMC1Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
11PSU7Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
12YYG1Mod. Nucleotide4-(3-[5-O-PHOSPHONORIBOFURANOSYL]-4,6-DIMETHYL-8-OXO-4,8-DIHYDRO-3H-1,3,4,5,7A-PENTAAZA-S-INDACEN-YLAMINO-BUTYRIC ACID METHYL ESTER

(-) Sites  (0, 0)

(no "Site" information available for 486D)

(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 486D)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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Chain A from PDB  Type:RNA  Length:74
                                                                                                           
                486d A    1 UCCGUGAUAGUUuAAuGGuCAGAAUgCCAGAcUGAAgAUcUGGAGAUcGGGGuuCAAUUCCCCGUCGCGGAGCC   75
                                    10  |  |  20     |  30 |    | 40     |||51  ||    61        71    
                                       13-PSU |     26-M2G |    |  |    46||    ||                    
                                          16-H2U          32-OMC|  |     48|    ||                    
                                             19-H2U            37-YYG     49-5MC||                    
                                                                  40-5MC       54-5MU                 
                                                                                55-PSU                


Chain B from PDB  Type:RNA  Length:3
                                    
                486d B    1 UUU    3


Chain C from PDB  Type:RNA  Length:72
                                                                                                         
                486d C    1 GCGGAUUUAgCUCAGuuGGGAGAGCgCCCGCuUGUCgCGUGGGAGgUCcUGUGuuCGaUCCACAGAAUUCGC   72
                                    10     || 20     |  30 |    | 40     |  50   ||  |60        70  
                                    10-2MG ||       26-M2G |    |       46-7MG   ||  |              
                                          16-H2U          32-PSU|          49-5MC||  |              
                                           17-H2U              37-1MG           54-5MU              
                                                                                 55-PSU             
                                                                                    58-1MA          


Chain D from PDB  Type:RNA  Length:3
                                    
                486d D    1 GUC    3


Chain E from PDB  Type:RNA  Length:72
                                                                                                         
                486d E    1 UCCGUGAUAGUUuAAuGGuCAGAAUGGGCGCuUGUCgCGUGCCAGAUcGGGGuuCAAUUCCCCGUCGCGGAG   73
                                    10  |  |  20        30 |    | 40     |||51  ||    61        71  
                                       13-PSU |           32-PSU|       46||    ||                  
                                          16-H2U               37-1MG    48|    ||                  
                                             19-H2U                       49-5MC||                  
                                                                               54-5MU               
                                                                                55-PSU              


Chain F from PDB  Type:RNA  Length:85
                                                                                                                      
                486d F 1404 CGUCACACCAUGGAAGGGGGUUGCAAAGAAAGGGUGGCCCCCUUCGGGGCGCCUAACUUUGUGAUUCCUAACUGGGGUGAAGUCG 1497
                                  1413      1423      1433      1443 ||   1462      1472      1482      1492     
                                                                  1445|                                          
                                                                   1455                                          


Chain G from PDB  Type:RNA  Length:33
                                                                  
                486d G  883 CUGGGGAGUACGGCCGCAAGGCUGAAACUCAAA  915
                                   892       902       912
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 486D)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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  486d
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