1IPR - JenaLib

Theoretical Model (Jmol Viewer)

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,_^#
( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Keywords :   Noncognate Codon Recognition, Small Ribosomal Rna, Large Ribosomal Rna, Mrna, Trna, Ef-Tu (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)

Molecule 1 - 16S RIBOSOMAL RNA
	Chains	:	A
	Organism Common	:	BACTERIA
	Organism Scientific	:	ESCHERICHIA COLI

*Molecule 2 - 5'- R(PUPUPUPUPUPUPUPGPUPUPUPUPUPUPUPUPUPUPU PU)-3'*
	Chains	:	B
	Organism Common	:	BACTERIA
	Organism Scientific	:	ESCHERICHIA COLI
	Other Details	:	MESSENGER RNA

Molecule 3 - TRNA BOUND TO P SITE
	Chains	:	C
	Organism Common	:	BACTERIA
	Organism Scientific	:	ESCHERICHIA COLI

Molecule 4 - TRNA BOUND TO R SITE
	Chains	:	D
	Organism Common	:	BACTERIA
	Organism Scientific	:	ESCHERICHIA COLI

Molecule 5 - 23S RIBOSOMAL RNA
	Chains	:	E
	Organism Common	:	BACTERIA
	Organism Scientific	:	ESCHERICHIA COLI

Molecule 6 - ELONGATION FACTOR G
	Chains	:	F
	Organism Common	:	BACTERIA
	Organism Scientific	:	THERMUS THERMOPHILUS

Molecule 7 - ELONGATION FACTOR TU
	Chains	:	G
	Organism Common	:	BACTERIA
	Organism Scientific	:	THERMUS AQUATICUS


Theoretical Model	:

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

Summary Information (see also Sequences/Alignments below)

Theoretical Model (12, 16)

No.	Name	Count	Type	Full Name
1	1MA	1	Mod. Nucleotide	6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
2	2MG	1	Mod. Nucleotide	2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
3	5MC	2	Mod. Nucleotide	5-METHYLCYTIDINE-5'-MONOPHOSPHATE
4	5MU	1	Mod. Nucleotide	5-METHYLURIDINE 5'-MONOPHOSPHATE
5	CYS	1	Mod. Amino Acid	CYSTEINE
6	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
7	H2U	2	Mod. Nucleotide	5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
8	M2G	1	Mod. Nucleotide	N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
9	OMC	1	Mod. Nucleotide	O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
10	OMG	2	Mod. Nucleotide	O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
11	PSU	2	Mod. Nucleotide	PSEUDOURIDINE-5'-MONOPHOSPHATE
12	YG	1	Mod. Residue	WYBUTOSINE

(no "Site" information available for 1IPR)

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

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

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

Theoretical Model (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TR_1	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.	EFTU_THEAQ	52-67	1	G:9051-9066
1	G_TR_1	PS00301		EFG_THETH	53-68	1	F:8068-8068

(no "Exon" information available for 1IPR)

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:166
                                                                                                                                                                                                       
                1ipr A 1046 AGGUGCUGCAUGACUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGgCCCU 1211
                                  1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205 |    
                                                                                                                                                                                          1207-OMG

Chain B from PDB  Type:RNA  Length:20
                                                     
                1ipr B 1623 UUUUUUUGUUUUUUUUUUUU 1642
                                  1632      1642

Chain C from PDB  Type:RNA  Length:92
                                                                                                                             
                1ipr C 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 D from PDB  Type:NUCLEIC  Length:67
                                                                                                    
                1ipr D 1901 GGCGCGUAACAAAGCGGAUGUAGCGGAUGCAACCGUCUAGUCCGGTCGACUCCGGAACGCGCCUCCA 1976
                                  1911    ||1924      1935|||   1948     |1959      1969       
                               1907|   1916|||     1931|  |||  1946|  1954|                    
                                1909    1918||      1933  |||   1948   1956                    
                                         1919|         1936||                                  
                                          1922          1938|                                  
                                                         1940

Chain E from PDB  Type:RNA  Length:29
                                                              
                1ipr E 4646 CUGCUCCUAGUACGAGAGGACCGGAGUGG 4674
                                  4655      4665

Chain F from PDB  Type:PROTEIN  Length:632
 aligned with EFG_THETH | P13551 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:685
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684     
           EFG_THETH      5 VEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLIK  689
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................................----------------------------............................................................................................................................................................................................................................................................................................................................................---------........--------....................---.......................-----...................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ipr F 8005 VEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRI----------------------------AVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVIL---------IDVAIEPK--------SQALARLAEEDPTFRVSTHP---QTIISGMGELHLEIIVDRLKREF-----VGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLIK 8689
                                  8014      8024      8034    |    -         -         -   |  8074      8084      8094      8104      8114      8124      8134      8144      8154      8164      8174      8184      8194      8204      8214      8224      8234      8244      8254      8264      8274      8284      8294      8304      8314      8324      8334      8344      8354      8364      8374      8384      8394    |    -    | 8414 |       -|     8434      8444   |  8454      8464     |   - |    8484      8494      8504      8514      8524      8534      8544      8554      8564      8574      8584      8594      8604      8614      8624      8634      8644      8654      8664      8674      8684     
                                                           8039                         8068                                                                                                                                                                                                                                                                                                                                       8399      8409   8416     8425               8444   |                  8470  8476                                                                                                                                                                                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    8448

Chain G 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
                1ipr G 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 '\|'

(no "SCOP Domain" information available for 1IPR)

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

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

Theoretical Model(hide GO term definitions)

Chain F (EFG_THETH | P13551)

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.

Chain G (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.

Theoretical Model
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	Ligands, Modified Residues, Ions
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	Sites
(no "Sites" information available for 1ipr)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ipr)

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	1ipr
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	EFTU_THEAQ \| Q01698
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1ip8	MODEL 1
1ipl	MODEL 2
1ipm	MODEL 3
1ipn	MODEL 4
1ipo	MODEL 5
1ipq	MODEL 6
1ipu	MODEL 8
1ipv	MODEL 9
1ipx	MODEL 10
1ipy	MODEL 11
1ipz	MODEL 12

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (12, 16)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (8, 16)

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