1MJ1 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   FITTING THE TERNARY COMPLEX OF EF-TU/TRNA/GTP AND RIBOSOMAL PROTEINS INTO A 13 A CRYO-EM MAP OF THE COLI 70S RIBOSOME

Authors :   H. Stark, M. V. Rodnina, H. -J. Wieden, F. Zemlin, W. Wintermeyer, M. Van

Date :   26 Aug 02 (Deposition) - 01 Nov 02 (Release) - 13 Jul 11 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   13.00

Chains :   Asym./Biol. Unit : A,C,D,L,O,P,Q,R

Keywords :   70S Ribosome, Low Resolution Model Ternary Complex, Ef-Tu, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Stark, M. V. Rodnina, H. -J. Wieden, F. Zemlin, W. Wintermeyer, M. Van Heel
Ribosome Interactions Of Aminoacyl-Trna And Elongation Factor Tu In The Codon Recognition Complex
Nat. Struct. Biol. V. 9 849 2002
PubMed-ID: 12379845

Molecule 1 - PHE-TRNA
	Chains	:	D, C
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	TAKEN FROM PDB ENTRIES 1GIX, 1TRA

Molecule 2 - SARCIN-RICIN LOOP OF 23SRRNA
	Chains	:	Q
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	TAKEN FROM PDB ENTRY 1GIY

Molecule 3 - HELIX 69 OF 23S RRNA
	Chains	:	R
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	TAKEN FROM PDB ENTRY 1GIY

Molecule 4 - ELONGATION FACTOR TU
	Chains	:	A
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	TAKEN FROM PDB ENTRY 1B23

Molecule 5 - S12 RIBOSOMAL PROTEIN
	Chains	:	O
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	TAKEN FROM PDB ENTRY 1GIX

Molecule 6 - S13 RIBOSOMAL PROTEIN
	Chains	:	P
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	TAKEN FROM PDB ENTRY 1GIX

Molecule 7 - L11 RIBOSOMAL PROTEIN
	Chains	:	L
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	TAKEN FROM PDB ENTRY 1GIY

		1	2	3	4	5	6	7	8
Asymmetric/Biological Unit	:	A	C	D	L	O	P	Q	R

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (11, 28)

No.	Name	Count	Type	Full Name
1	1MA	2	Mod. Nucleotide	6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
2	2MG	2	Mod. Nucleotide	2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
3	5MC	4	Mod. Nucleotide	5-METHYLCYTIDINE-5'-MONOPHOSPHATE
4	5MU	2	Mod. Nucleotide	5-METHYLURIDINE 5'-MONOPHOSPHATE
5	7MG	2	Mod. Nucleotide	7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
6	H2U	4	Mod. Nucleotide	5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
7	M2G	2	Mod. Nucleotide	N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
8	OMC	2	Mod. Nucleotide	O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
9	OMG	2	Mod. Nucleotide	O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
10	PSU	4	Mod. Nucleotide	PSEUDOURIDINE-5'-MONOPHOSPHATE
11	YG	2	Mod. Residue	WYBUTOSINE

(no "Site" information available for 1MJ1)

(no "SS Bond" information available for 1MJ1)

(no "Cis Peptide Bond" information available for 1MJ1)

(no "SAP(SNP)/Variant" information available for 1MJ1)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S13_2	PS50159	Ribosomal protein S13 family profile.	RS13_THET8	4-112	1	P:3-111
2	G_TR_1	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.	EFTU_THEAQ	52-67	1	A:51-66
3	RIBOSOMAL_S13_1	PS00646	Ribosomal protein S13 signature.	RS13_THET8	88-101	1	P:87-100

(no "Exon" information available for 1MJ1)

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 A 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 d1mj1a_ A: 70S ribosome functional complex                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee.....hhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhh......eeeeee...eeeeeee...hhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhhhhhhhhhh........eee.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh............eeeeeeeeee...eeeeeeeeee.eee...eeeee......eeeeeeeee.......eee...eeeeee...hhhhh....eee.......eeeeeeeeee.hhhhh............eeee..eeeeeeeee...........eeeeeeeeeeee......eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mj1 A   1 AKGEFIRTKRHVNVGTIGHVDHGKTTLTAALTYVAAAENRNVEVKDYGDIDKAREERARGITINTAHVEYETAKRHYSHVDCRGHADYIKNMITGAAQMDGAILVVSAADGRMRQTREHILLARQVGVRYIVVFMNKVDMVDDRELLDLVEMEVRDLLNQYEFRGDEVRVIRGSALLALEEMHKNRKTKRGENEWVDKIWELLDAIDEYIRTRVRDVDKRFLMRVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLARETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKRGSITRHTKFEASVYILKKEEGGRHTGFFTGYRRQFYFRTTDVTGVVRLRQGVEMVMRGDNVTFTVELIKRVALEEGLRFAIREGGRTVGAGVVTKILE 405
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400

Chain C from PDB  Type:RNA  Length:76
                                                                                                            
                 1mj1 C   1 GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAGgUCcUGUGuuCGaUCCACAGAAUUCGCACCA  76
                                    10     || 20     |  30 | |  | 40     |  50   ||  |60        70      
                                    10-2MG ||       26-M2G | |  | ||     |  |    55-PSU                 
                                          16-H2U          32-OMC| ||     |  |    |  58-1MA              
                                           17-H2U           34-OMG||     |  |    |                      
                                                               37-YG     |  |    |                      
                                                                 39-PSU  |  |    |                      
                                                                  40-5MC |  |    |                      
                                                                        46-7MG   |                      
                                                                           49-5MC|                      
                                                                                54-5MU

Chain D from PDB  Type:RNA  Length:76
                                                                                                            
                 1mj1 D   1 GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAGgUCcUGUGuuCGaUCCACAGAAUUCGCACCA  76
                                    10     || 20     |  30 | |  | 40     |  50   ||  |60        70      
                                    10-2MG ||       26-M2G | |  | ||     |  |    55-PSU                 
                                          16-H2U          32-OMC| ||     |  |    |  58-1MA              
                                           17-H2U           34-OMG||     |  |    |                      
                                                               37-YG     |  |    |                      
                                                                 39-PSU  |  |    |                      
                                                                  40-5MC |  |    |                      
                                                                        46-7MG   |                      
                                                                           49-5MC|                      
                                                                                54-5MU

Chain L from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains d1mj1l_ L: 70S ribosome functional complex                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mj1 L   1 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain O from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d1mj1o_ O: 70S ribosome functional complex                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mj1 O   1 PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEA 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain P from PDB  Type:PROTEIN  Length:125
 aligned with RS13_THET8 | P80377 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:125
                                    11        21        31        41        51        61        71        81        91       101       111       121     
           RS13_THET8     2 ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK 126
               SCOP domains d1mj1p_ P: 70S ribosome functional complex                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --RIBOSOMAL_S13_2  PDB: P:3-111 UniProt: 4-112                                                                 -------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------RIBOSOMAL_S13_------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mj1 P   1 ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK 125
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain Q from PDB  Type:RNA  Length:41
                                                                         
                 1mj1 Q   1 GGGGGGCUCUUCCUAGUACGAGAGGACCGGAAGGGACGCAC  41
                                    10        20        30        40

Chain R from PDB  Type:RNA  Length:27
                                                           
                 1mj1 R   1 GCGGCCGUAACUAUAACGGUCCUAAGG  27
                                    10        20

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Low resolution protein structures (283)

Fold: Ribosome and ribosomal fragments (154)

Superfamily: Ribosome and ribosomal fragments (154)

Family: Ribosome complexes (103)

Protein domain: 70S ribosome functional complex (103)

Escherichia coli [TaxId: 562] (72)

1a	d1mj1a_	A:
1b	d1mj1l_	L:
1c	d1mj1o_	O:
1d	d1mj1p_	P:

(no "CATH Domain" information available for 1MJ1)

(no "Pfam Domain" information available for 1MJ1)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Chain P (RS13_THET8 | P80377)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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: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.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1MJ1)

Description

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Chains, Units

Ligands, Modified Residues, Ions (11, 28)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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PROSITE Motifs (3, 3)

Exons (0, 0)

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SCOP Domains (1, 4)

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Gene Ontology (31, 60)

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