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(-)Theoretical Model
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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  RIBOSOMAL RNAS AND PROTEINS AS WELL AS FACTORS
 
Authors :  K. Nagano, N. Nagano
Date :  17 May 01  (Deposition) - 30 Sep 03  (Release) - 30 Sep 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C,D,E,F,G,H,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Proofreading, Gtp Hydrolysis, Ef-Tu, Small Ribosomal Rna, Large Ribosomal Rna, Mrna, Trna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Nagano, N. Nagano
Stereochemical Mechanism Of Translocation, Termination And Codon Recognition Of E. Coli 16S And 23S Ribosomal Rnas
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 16S RIBOSOMAL RNA
    Chains: A
    Organism Common: BACTERIA
    Organism Scientific: ESCHERICHIA COLI
 
Molecule 2 - 5'- R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U P*U)-3'
    Chains: B
    Organism Common: BACTERIA
    Organism Scientific: ESCHERICHIA COLI
    Other Details: MESSENGER RNA
 
Molecule 3 - TRNAS BOUND TO E, P, AND R SITES
    Chains: C, D, E
    Organism Common: BACTERIA
    Organism Scientific: ESCHERICHIA COLI
 
Molecule 4 - 23S RIBOSOMAL RNA
    Chains: F
    Organism Common: BACTERIA
    Organism Scientific: ESCHERICHIA COLI
 
Molecule 5 - NASCENT POLYPEPTIDE
    Chains: G
    Organism Common: BACTERIA
    Organism Scientific: ESCHERICHIA COLI
 
Molecule 6 - ELONGATION FACTOR TU
    Chains: H
    Organism Common: BACTERIA
    Organism Scientific: THERMUS AQUATICUS

 Structural Features

(-) Chains, Units

  
Theoretical Model : 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (14, 48)

Theoretical Model (14, 48)
No.NameCountTypeFull Name
11MA3Mod. Nucleotide6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
22MG3Mod. Nucleotide2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
32MU1Mod. Nucleotide2',5-DIMETHYLURIDINE-5'-MONOPHOSPHATE
45MC6Mod. Nucleotide5-METHYLCYTIDINE-5'-MONOPHOSPHATE
55MU3Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
6CYS1Mod. Amino AcidCYSTEINE
7GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
8H2U6Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
9M2G3Mod. NucleotideN2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
10OMC5Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
11OMG3Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
12OMU2Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE
13PSU8Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
14YG3Mod. ResidueWYBUTOSINE

(-) Sites  (0, 0)

(no "Site" information available for 1IPU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.EFTU_THEAQ52-67  1H:9051-9066

(-) Exons   (0, 0)

(no "Exon" information available for 1IPU)

(-) Sequences/Alignments

Theoretical Model
   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:RNA  Length:148
                                                                                                                                                                                     
                1ipu A 1055 AUGACUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAU 1202
                                  1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194        


Chain B from PDB  Type:RNA  Length:20
                                                     
                1ipu B 1623 UUUUUUUUUUUUUUUUUUUU 1642
                                  1632      1642


Chain C from PDB  Type:RNA  Length:92
                                                                                                                             
                1ipu C 1701 GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAAUGCGGUCAAAAGCUGCAUCcUGUGuuCGaUCCACAGAAUUCGCACCA 1792
                                  1710     |1720     |1730 | |  1740      1750      1760    | 1770|  |  1780      1790  
                                  1710-2MG ||     1726-M2G | |  | ||                     1765-5MC||  |                  
                                        1716-H2U        1732-OMC| ||                          1770-5MU                  
                                         1717-H2U         1734-OMG||                           1771-PSU                 
                                                             1737-YG                              1774-1MA              
                                                               1739-PSU                                                 
                                                                1740-5MC                                                


Chain D from PDB  Type:RNA  Length:92
                                                                                                                             
                1ipu D 1801 GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAAUGCGGUCAAAAGCUGCAUCcUGUGuuCGaUCCACAGAAUUCGCACCA 1892
                                  1810     |1820     |1830 | |  1840      1850      1860    | 1870|  |  1880      1890  
                                  1810-2MG ||     1826-M2G | |  | ||                     1865-5MC||  |                  
                                        1816-H2U        1832-OMC| ||                          1870-5MU                  
                                         1817-H2U         1834-OMG||                           1871-PSU                 
                                                             1837-YG                              1874-1MA              
                                                               1839-PSU                                                 
                                                                1840-5MC                                                


Chain E from PDB  Type:RNA  Length:92
                                                                                                                             
                1ipu E 1901 GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAAUGCGGUCAAAAGCUGCAUCcUGUGuuCGaUCCACAGAAUUCGCACCA 1992
                                  1910     |1920     |1930 | |  1940      1950      1960    | 1970|  |  1980      1990  
                                  1910-2MG ||     1926-M2G | |  | ||                     1965-5MC||  |                  
                                        1916-H2U        1932-OMC| ||                          1970-5MU                  
                                         1917-H2U         1934-OMG||                           1971-PSU                 
                                                             1937-YG                              1974-1MA              
                                                               1939-PSU                                                 
                                                                1940-5MC                                                


Chain F from PDB  Type:RNA  Length:782
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                1ipu F 2406 GGGGGGACCAUCCUCCACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGuAACuAuAACGGUCCUAAGGUAGCGAAAuUCCUUGUCGGGUAAGUUCCGACcUGCACGAAUGGCGUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCAcCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCuGUUCGCCAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCC 4788
                                  2415     |3832      3842      3852      3862      3872      3882      3892      3902      3912  | | 3922      3932      3942      3952      3962      3972   || 4028      4038      4048      4058      4068      4078      4236      4246      4256      4266      4276      4286      4296      4306      4316      4326      4336      4346      4356      4366      4376      4386      4396      4406      4416      4426      4436      4446      4456      4466      4476      4486      4496 |    4506      4516      4526      4536      4546     |4556      4566      4576      4586      4596      4606      4616      4626      4636      4646      4656      4666      4676      4686      4696      4706      4716      4726      4736      4746      4756      4766      4776      4786  
                                        2421|                                                                              3911-PSU |                  3939-2MU               3962-OMC      3976|                                                          4085|                                                                                                                                                                                                                                                                    4498-OMC                                              4552-OMU                                                                                                                                                                                                                                        
                                         3829                                                                                  3915-OMU                                                      4023                                                           4234                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                                                                                                                                 3917-PSU                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain G from PDB  Type:PROTEIN  Length:19
                                                    
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ................... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                1ipu G 5001 YKKKKKKKKKKKKKKKKYY 5019
                                  5010         


Chain H from PDB  Type:PROTEIN  Length:405
 aligned with EFTU_THEAQ | Q01698 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:405
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401     
          EFTU_THEAQ      2 AKGEFIRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE  406
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................................................................................................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ipu H 9001 AKGEFIRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 9405
                                  9010      9020      9030      9040      9050      9060      9070      9080      9090      9100      9110      9120      9130      9140      9150      9160      9170      9180      9190      9200      9210      9220      9230      9240      9250      9260      9270      9280      9290      9300      9310      9320      9330      9340      9350      9360      9370      9380      9390      9400
   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 1IPU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Theoretical Model(hide GO term definitions)
Chain H   (EFTU_THEAQ | Q01698)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at 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.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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  1ipu
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  EFTU_THEAQ | Q01698
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 Related Entries

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

UniProtKB/Swiss-Prot
        EFTU_THEAQ | Q01698: 1b23 1eft 1h1u 1ipm 1ipo 1ipq 1ipr 1l1u 1mj1 1ob5 1ttt 1tui

(-) Related Entries Specified in the PDB File

1ip8 MODEL 1
1ipl MODEL 2
1ipm MODEL 3
1ipn MODEL 4
1ipo MODEL 5
1ipq MODEL 6
1ipr MODEL 7
1ipv MODEL 9
1ipx MODEL 10
1ipy MODEL 11
1ipz MODEL 12