9B4Z: E. coli 70S ribosome complex

Name: PDB 9B4Z: E. coli 70S ribosome complex (N1-methylated 16S A1408 + arbekacin)
Published: 2025-08-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

E. coli 70S ribosome complex (N1-methylated 16S A1408 + arbekacin). Determined by electron microscopy at 2.2 Å resolution. Released 27 Aug 2025.

Method: Electron microscopy
Resolution: 2.2 Å
Organism: Escherichia coli
Chains: 56
Atoms: 146,493
Mol. weight: 2249.97 kDa
Ligands: ZN, 84G, MG
Released: 27 Aug 2025

Explore 9B4Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B4Z contains 237 α-helices and 321 β-strands across 49 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 AB: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	25-30	6
β-strand	31	1	4
α-helix	35-37	3
β-strand	41	1	4
α-helix	43-62	20
β-strand	69-70	2	5
α-helix	76-85	10
α-helix	86-88	3
β-strand	91-92	2	5
α-helix	96-97	2
α-helix	104-120	17
α-helix	132-147	16
β-strand	161-163	3	5
α-helix	170-179	10
β-strand	183-187	5	5
β-strand	198-201	4	5
α-helix	207-222	16

Chain AC: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	17-18	2
β-strand	20	1	8
α-helix	29-46	18
α-helix	48-50	3
β-strand	52-56	5	9
β-strand	57	1	8
β-strand	64	1	10
β-strand	67-70	4	9
α-helix	73-77	5
α-helix	82-95	14
β-strand	99	1	10
β-strand	102-105	4	9
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-142	13
β-strand	150-154	5	11
α-helix	157-159	3
β-strand	168-169	2	11
β-strand	182	1	12
β-strand	185-189	5	11
β-strand	196-201	6	11
β-strand	203	1	12

Chain AD: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	50-65	16
α-helix	69-81	13
α-helix	86-95	10
β-strand	97	1	14
α-helix	98-105	8
α-helix	111-119	9
β-strand	123-125	3	15
β-strand	128-129	2	15
α-helix	135	1
β-strand	136	1	14
α-helix	137	1
β-strand	141-145	5	15
α-helix	147-150	4
α-helix	153-161	9
α-helix	162-164	3
β-strand	171	1	15
β-strand	179-182	4	15
α-helix	185-187	3
α-helix	188-190	3
α-helix	198-205	8

Chain AE: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	13-22	10	18
β-strand	25	1	19
β-strand	28	1	19
β-strand	31-40	10	18
β-strand	46-49	4	18
β-strand	52-53	2	18
α-helix	56-68	13
β-strand	71-72	2	18
β-strand	77	1	20
β-strand	80	1	20
β-strand	85-89	5	21
β-strand	92-96	5	21
β-strand	97	1	22
α-helix	112-118	7
β-strand	124	1	22
β-strand	128-129	2	21
α-helix	133-136	4
α-helix	141-144	4
α-helix	150-157	8

Chain AF: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	24
β-strand	4-10	7	25
α-helix	12-17	6
α-helix	18-31	14
β-strand	35-36	2	24
β-strand	40-45	6	25
β-strand	57-61	5	25
β-strand	64-66	3	24
α-helix	68-80	13
β-strand	84-91	8	25

Chain AG: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-30	10
α-helix	36-54	19
α-helix	58-67	10
β-strand	73-77	5	26
β-strand	86-90	5	26
α-helix	91-92	2
α-helix	93-110	18
α-helix	116-128	13
α-helix	133-147	15

Chain AH: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	24-28	5	27
α-helix	31-42	12
β-strand	46-52	7	27
β-strand	58-63	6	27
β-strand	75-77	3	28
β-strand	80	1	29
β-strand	83	1	29
β-strand	86-87	2	28
α-helix	89-91	3
β-strand	101-106	6	28
β-strand	109-112	4	28
α-helix	113-119	7
β-strand	123-129	7	28

Chain AI: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	39
β-strand	11-12	2	39
β-strand	15-22	8	39
β-strand	28-30	3	39
β-strand	34	1	39
α-helix	35	1
α-helix	36-40	5
α-helix	50-53	4
β-strand	62-68	7	39
α-helix	72-86	15
α-helix	87-89	3
α-helix	95-101	7
α-helix	110-114	5
β-strand	120	1	40
β-strand	123	1	40

41 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	AA	RNA	1539	Escherichia coli
30S ribosomal protein S2	AB	protein	240	Escherichia coli	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	AC	protein	233	Escherichia coli	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	AD	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	AE	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	AF	protein	135	Escherichia coli	P02358
30S ribosomal protein S7	AG	protein	179	Escherichia coli	P02359
30S ribosomal protein S8	AH	protein	130	Escherichia coli	P0A7W7
30S ribosomal protein S9	AI	protein	130	Escherichia coli	P0A7X3
30S ribosomal protein S10	AJ	protein	103	Escherichia coli	P0A7R5
30S ribosomal protein S11	AK	protein	129	Escherichia coli	P0A7R9
30S ribosomal protein S12	AL	protein	124	Escherichia coli	P0A7S3

43 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>9B4Z_1 16S ribosomal RNA (chains AA)
AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAG
UCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAU
GUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUA
ACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGG
GAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAG
GAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGG
GAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUU
CGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUG
ACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGG
GUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAG
AUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCG
UAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG
GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAA
ACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCC
UUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAA
GGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUU
CGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGA
AUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAA
AUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCC
GGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA
UCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGA
CCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACU
CGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUU
CCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUA
GCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAAC
AAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU

Sequence of entity 2 (AB), FASTA

>9B4Z_2 30S ribosomal protein S2 (chains AB)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA

Sequence of entity 3 (AC), FASTA

>9B4Z_3 30S ribosomal protein S3 (chains AC)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (AD), FASTA

>9B4Z_4 30S ribosomal protein S4 (chains AD)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (AE), FASTA

>9B4Z_5 30S ribosomal protein S5 (chains AE)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (AF), FASTA

>9B4Z_6 30S ribosomal protein S6 (chains AF)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (AG), FASTA

>9B4Z_7 30S ribosomal protein S7 (chains AG)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (AH), FASTA

>9B4Z_8 30S ribosomal protein S8 (chains AH)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (AI), FASTA

>9B4Z_9 30S ribosomal protein S9 (chains AI)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (AJ), FASTA

>9B4Z_10 30S ribosomal protein S10 (chains AJ)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (AK), FASTA

>9B4Z_11 30S ribosomal protein S11 (chains AK)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV

Sequence of entity 12 (AL), FASTA

>9B4Z_12 30S ribosomal protein S12 (chains AL)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
84G	Arbekacin	C22 H44 N6 O10	2
MG	Magnesium ion	Mg	309

Primary citation

Basis for selective drug evasion of an aminoglycoside-resistance ribosomal RNA modification. Dey, D., Mattingly, J.M., Zelinskaya, N. et al. Nat Commun (2025) 16:7992-7992. DOI 10.1038/s41467-025-63278-5 · 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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