9Q3R: Escherichia coli 70S ribosome

Name: PDB 9Q3R: Cryo-EM structure of the Escherichia coli 70S ribosome bound to mRNA, P-site fMet-tRNAfMet, glycyl-tRNAGly in A/T conformation, EF-Tu-GDPCP, and bottromycin at 1.99A resolution
Published: 2026-08-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of the Escherichia coli 70S ribosome bound to mRNA, P-site fMet-tRNAfMet, glycyl-tRNAGly in A/T conformation, EF-Tu-GDPCP, and bottromycin at 1.99A resolution. Determined by electron microscopy at 1.99 Å resolution. Released 26 Aug 2026.

Method: Electron microscopy
Resolution: 1.99 Å
Organism: Escherichia coli
Chains: 57
Atoms: 151,455
Mol. weight: 2283.38 kDa
Ligands: ZN, MQH, GCP, MG
Released: 26 Aug 2026

Explore 9Q3R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q3R contains 284 α-helices and 322 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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	3-7	5
α-helix	11-33	23
α-helix	41-60	20

Chain 2: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	94
α-helix	18-27	10
β-strand	35-39	5	94
α-helix	42-50	9
α-helix	52-54	3
β-strand	55-58	4	94

Chain 3: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	95
β-strand	21-26	6	95
β-strand	32-33	2	95
α-helix	42-45	4
α-helix	56-63	8

Chain 4: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-16	7
α-helix	17-19	3
α-helix	21-25	5
β-strand	29-30	2	1
β-strand	37-38	2	1
β-strand	42	1	62
β-strand	48-49	2	2
β-strand	52-53	2	2

Chain 5: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	14
β-strand	20-25	6	14
α-helix	33-34	2
β-strand	35-40	6	14
β-strand	45-52	8	14

Chain 6: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-22	5
α-helix	25-37	13

Chain 7: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	14-16	3	23
β-strand	22-24	3	23
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	23
α-helix	50-51	2
α-helix	52-61	10

Chain 8: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	30
β-strand	14-19	6	30
β-strand	22-27	6	30
α-helix	31-33	3
β-strand	35-37	3	30

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	J7QM75 (AlphaFold model)
Small ribosomal subunit protein uS3	c	protein	233	Escherichia coli	B7MCS9 (AlphaFold model)
Small ribosomal subunit protein uS4	d	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
Small ribosomal subunit protein uS5	e	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	f	protein	131	Escherichia coli	C3SFQ7
30S ribosomal protein S7	g	protein	156	Escherichia coli	P02359
Small ribosomal subunit protein uS8	h	protein	130	Escherichia coli	C3SR12
Small ribosomal subunit protein uS9	i	protein	130	Escherichia coli	C3SRY2
Small ribosomal subunit protein uS10	j	protein	103	Escherichia coli	C3SQT7
Small ribosomal subunit protein uS11	k	protein	129	Escherichia coli	A7ZSI6
Small ribosomal subunit protein uS12	l	protein	124	Escherichia coli	A0A0F1AUC4

45 more molecules are not listed.

Sequence of entity 1 (a), FASTA

>9Q3R_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

>9Q3R_2 30S ribosomal protein S2 (chains b)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFEKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (c), FASTA

>9Q3R_3 Small ribosomal subunit protein uS3 (chains c)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (d), FASTA

>9Q3R_4 Small ribosomal subunit protein uS4 (chains d)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (e), FASTA

>9Q3R_5 Small ribosomal subunit protein uS5 (chains e)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (f), FASTA

>9Q3R_6 30S ribosomal protein S6 (chains f)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEE

Sequence of entity 7 (g), FASTA

>9Q3R_7 30S ribosomal protein S7 (chains g)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRW

Sequence of entity 8 (h), FASTA

>9Q3R_8 Small ribosomal subunit protein uS8 (chains h)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (i), FASTA

>9Q3R_9 Small ribosomal subunit protein uS9 (chains i)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (j), FASTA

>9Q3R_10 Small ribosomal subunit protein uS10 (chains j)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (k), FASTA

>9Q3R_11 Small ribosomal subunit protein uS11 (chains k)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHDG
CRPPKKRRV

Sequence of entity 12 (l), FASTA

>9Q3R_12 Small ribosomal subunit protein uS12 (chains l)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MQH	Bottromycin A2	C42 H62 N8 O7 S	1
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
MG	Magnesium ion	Mg	1007

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

Primary citation

Sequence-specific trapping of EF-Tu/glycyl-tRNA complex on the ribosome by bottromycin. Travin, D.Y., Basu, R.S., Paranjpe, M. et al. To be published.

Other PDB entries of the same protein (UniProt J7QM75 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9Q3Q 2.01 Å, Cryo-EM structure of translating Escherichia coli 70S ribosome bound to mRNA, P-site…
9ZN2 3.0 Å, Escherichia coli 70S ribosome initiation complex bound to IF1 and extended IF2-GDPCP…

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