9ZN2: Escherichia coli 70S ribosome initiation complex

Name: PDB 9ZN2: Escherichia coli 70S ribosome initiation complex bound to IF1 and extended IF2-GDPCP (70S IC*)
Published: 2026-09-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Escherichia coli 70S ribosome initiation complex bound to IF1 and extended IF2-GDPCP (70S IC*). Determined by electron microscopy at 3.0 Å resolution. Released 30 Sept 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Escherichia coli, Escherichia phage T4
Chains: 56
Atoms: 145,464
Mol. weight: 2284.18 kDa
Ligands: ZN, GCP, FME, MG
Released: 30 Sept 2026

Explore 9ZN2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ZN2 contains 257 α-helices and 367 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	11-34	24
α-helix	42-58	17

Chain 2: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	111
α-helix	20-27	8
β-strand	35-38	4	111
α-helix	42-50	9
α-helix	52-54	3
β-strand	55-58	4	111

Chain 3: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	113
β-strand	14-16	3	114
β-strand	20-22	3	114
β-strand	25-26	2	113
β-strand	32-34	3	114
α-helix	42-45	4
α-helix	59-63	5

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	23-25	3
β-strand	29-30	2	115
β-strand	37-38	2	115
β-strand	42	1	68
β-strand	48-49	2	116
β-strand	52-53	2	116

Chain 5: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	1
β-strand	20-25	6	1
α-helix	33-34	2
β-strand	35-40	6	1
β-strand	45-53	9	1

Chain 6: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-21	4
α-helix	25-37	13

Chain 7: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	10-12	3
β-strand	15-16	2	20
β-strand	22-23	2	20
α-helix	38-43	6
α-helix	55-61	7

Chain 8: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	25
β-strand	15-19	5	25
β-strand	22-26	5	25
α-helix	31-33	3
β-strand	35-37	3	25

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)
30S ribosomal protein S3	c	protein	233	Escherichia coli	P0A7V3 (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

44 more molecules are not listed.

Sequence of entity 1 (a), FASTA

>9ZN2_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

>9ZN2_2 30S ribosomal protein S2 (chains b)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFEKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (c), FASTA

>9ZN2_3 30S ribosomal protein S3 (chains c)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (d), FASTA

>9ZN2_4 Small ribosomal subunit protein uS4 (chains d)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (e), FASTA

>9ZN2_5 Small ribosomal subunit protein uS5 (chains e)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (f), FASTA

>9ZN2_6 30S ribosomal protein S6 (chains f)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEE

Sequence of entity 7 (g), FASTA

>9ZN2_7 30S ribosomal protein S7 (chains g)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRW

Sequence of entity 8 (h), FASTA

>9ZN2_8 Small ribosomal subunit protein uS8 (chains h)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (i), FASTA

>9ZN2_9 Small ribosomal subunit protein uS9 (chains i)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (j), FASTA

>9ZN2_10 Small ribosomal subunit protein uS10 (chains j)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (k), FASTA

>9ZN2_11 Small ribosomal subunit protein uS11 (chains k)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHDG
CRPPKKRRV

Sequence of entity 12 (l), FASTA

>9ZN2_12 Small ribosomal subunit protein uS12 (chains l)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
FME	N-formylmethionine	C6 H11 N O3 S	1
MG	Magnesium ion	Mg	301

Primary citation

Time-resolved visualization of IF1- and IF2-driven translation initiation in bacteria. Guerra, G.S., Zafar, H., Ge, X. 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:

9Q3R 1.99 Å, Cryo-EM structure of the Escherichia coli 70S ribosome bound to mRNA, P-site…
9Q3Q 2.01 Å, Cryo-EM structure of translating Escherichia coli 70S ribosome bound to mRNA, P-site…

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