8G7P: Escherichia coli 70S ribosome

Name: PDB 8G7P: Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and Ile-tRNAIle(LAU) bound to the cognate AUA codon (Structure I)
Published: 2024-03-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and Ile-tRNAIle(LAU) bound to the cognate AUA codon (Structure I). Determined by electron microscopy at 2.9 Å resolution. Released 6 Mar 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Escherichia coli, Escherichia phage T4
Chains: 58
Atoms: 151,823
Mol. weight: 2301.45 kDa
Ligands: MG, ILE, GCP, ZN
Released: 6 Mar 2024

Explore 8G7P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G7P contains 230 α-helices and 325 β-strands across 51 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 1: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-32	22
α-helix	41-59	19

Chain 2: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	98
α-helix	18-27	10
β-strand	35-39	5	98
α-helix	42-48	7
α-helix	49-54	6
β-strand	55-58	4	98

Chain 3: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	1
β-strand	21-26	6	1
β-strand	32-34	3	1
α-helix	42-45	4
α-helix	56-63	8

Chain 4: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-16	7
α-helix	17-19	3
β-strand	29-30	2	4
β-strand	37-38	2	4
β-strand	48-49	2	5
β-strand	52-53	2	5

Chain 5: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	17
β-strand	20-25	6	17
β-strand	35-40	6	17
β-strand	45-52	8	17

Chain 6: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-21	4
α-helix	28-37	10

Chain 7: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	15-16	2	28
β-strand	22-24	3	28
α-helix	38-42	5
β-strand	48-49	2	28
α-helix	55-61	7

Chain 8: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	33
β-strand	14-18	5	33
β-strand	23-27	5	33
α-helix	31-33	3
β-strand	35-37	3	33

43 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
16S Ribosomal RNA	a	RNA	1542	Escherichia coli
30S ribosomal protein S2	b	protein	241	Escherichia coli	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	c	protein	233	Escherichia coli	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	d	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	e	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	f	protein	131	Escherichia coli	P02358
30S ribosomal protein S7	g	protein	156	Escherichia coli	P02359
30S ribosomal protein S8	h	protein	130	Escherichia coli	P0A7W7
30S ribosomal protein S9	i	protein	130	Escherichia coli	P0A7X3
30S ribosomal protein S10	j	protein	103	Escherichia coli	P0A7R5
30S ribosomal protein S11	k	protein	129	Escherichia coli	P0A7R9
30S ribosomal protein S12	l	protein	124	Escherichia coli	P0A7S3

45 more molecules are not listed.

Sequence of entity 1 (a), FASTA

>8G7P_1 16S Ribosomal RNA (chains a)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA

Sequence of entity 2 (b), FASTA

>8G7P_2 30S ribosomal protein S2 (chains b)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFEKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (c), FASTA

>8G7P_3 30S ribosomal protein S3 (chains c)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (d), FASTA

>8G7P_4 30S ribosomal protein S4 (chains d)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (e), FASTA

>8G7P_5 30S ribosomal protein S5 (chains e)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (f), FASTA

>8G7P_6 30S ribosomal protein S6 (chains f)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEE

Sequence of entity 7 (g), FASTA

>8G7P_7 30S ribosomal protein S7 (chains g)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRW

Sequence of entity 8 (h), FASTA

>8G7P_8 30S ribosomal protein S8 (chains h)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (i), FASTA

>8G7P_9 30S ribosomal protein S9 (chains i)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (j), FASTA

>8G7P_10 30S ribosomal protein S10 (chains j)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (k), FASTA

>8G7P_11 30S ribosomal protein S11 (chains k)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHDG
CRPPKKRRV

Sequence of entity 12 (l), FASTA

>8G7P_12 30S ribosomal protein S12 (chains l)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	876
ILE	Isoleucine	C6 H13 N O2	2
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
ZN	Zinc ion	Zn	2

Water and common crystallization additives (K) are not listed.

Primary citation

Structures of the ribosome bound to EF-Tu-isoleucine tRNA elucidate the mechanism of AUG avoidance. Rybak, M.Y., Gagnon, M.G. Nat Struct Mol Biol (2024) 31:810-816. DOI 10.1038/s41594-024-01236-3 · PubMed

Other PDB entries of the same protein (UniProt P0A7V0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8B0X 1.55 Å, Translating 70S ribosome in the unrotated state (P and E, tRNAs)
9Q87 1.55 Å, Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom…
4ODN 1.6 Å, Structure of SlyD from Thermus thermophilus in complex with S2-plus peptide
7OXH 1.7 Å, ttSlyD with pseudo-wild-type S2 peptide
4ODP 1.75 Å, Structure of SlyD delta-IF from Thermus thermophilus in complex with S2-W23A peptide
4ODM 1.75 Å, Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide
8CGJ 1.79 Å, Streptomycin bound to the 30S body
8CF1 1.82 Å, Tetracycline bound to the 30S head
7OXJ 1.85 Å, ttSlyD with M8A pseudo-wild-type S2 peptide
8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
9GHE 1.87 Å, Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S…
9T0Y 1.87 Å, E. coli 70S ribosome from delta-9 strain

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