9SS6: 70S ribosome from RimM-KO

Name: PDB 9SS6: 70S ribosome from RimM-KO
Published: 2026-02-04
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

70S ribosome from RimM-KO. Determined by electron microscopy at 2.6 Å resolution. Released 4 Feb 2026.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Escherichia coli
Chains: 55
Atoms: 144,877
Mol. weight: 2188.48 kDa
Released: 4 Feb 2026

Explore 9SS6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9SS6 contains 237 α-helices and 329 β-strands across 52 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 AA: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
β-strand	15-18	4	1
α-helix	24-26	3
β-strand	32-34	3	1
β-strand	37-39	3	1
α-helix	42-60	19
β-strand	66-69	4	2
α-helix	78-85	8
β-strand	89-91	3	2
α-helix	103-119	17
α-helix	124-127	4
α-helix	130-147	18
β-strand	159-163	5	2
α-helix	169-178	10
β-strand	182-186	5	2
α-helix	192-194	3
β-strand	197-200	4	2
α-helix	206-223	18

Chain AB: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	19-20	2	4
α-helix	29-45	17
α-helix	47-49	3
β-strand	51-57	7	4
β-strand	63-69	7	4
α-helix	72-75	4
α-helix	82-94	13
β-strand	98-102	5	4
α-helix	108-110	3
α-helix	112-124	13
α-helix	129-142	14
β-strand	147-154	8	5
β-strand	163-170	8	5
β-strand	179-190	12	5
β-strand	193-205	13	5

Chain AC: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-14	8
α-helix	44-45	2
α-helix	49-64	16
α-helix	68-80	13
α-helix	85-95	11
β-strand	96	1	6
α-helix	97-103	7
α-helix	110-118	9
β-strand	122-124	3	7
β-strand	127-128	2	7
α-helix	134	1
β-strand	135	1	6
α-helix	136-137	2
β-strand	140-144	5	7
α-helix	154-161	8
β-strand	170-172	3	7
β-strand	178-181	4	7
α-helix	184-185	2
α-helix	197-202	6

Chain AD: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	9
β-strand	14-21	8	10
β-strand	24	1	11
β-strand	27	1	11
β-strand	30-38	9	10
β-strand	39	1	9
β-strand	44-48	5	10
β-strand	51-52	2	10
α-helix	55-67	13
β-strand	70-72	3	10
β-strand	76	1	12
β-strand	79	1	12
β-strand	84-85	2	13
β-strand	88	1	14
β-strand	91	1	14
β-strand	94-96	3	13
β-strand	105	1	13
α-helix	111-117	7
β-strand	123-125	3	13
β-strand	128	1	14
α-helix	132-145	14
α-helix	149-155	7

Chain AE: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	16
β-strand	7-10	4	17
α-helix	13-17	5
α-helix	18-31	14
β-strand	36	1	18
β-strand	43-44	2	17
β-strand	58-61	4	17
β-strand	64	1	18
β-strand	65-66	2	16
α-helix	68-80	13
β-strand	84-88	5	17

Chain AF: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	20-29	10
α-helix	35-53	19
α-helix	58-66	9
β-strand	72-76	5	22
β-strand	85-89	5	22
α-helix	92-107	16
α-helix	115-127	13
α-helix	132-146	15

Chain AG: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	23-27	5	32
α-helix	30-42	13
β-strand	46-51	6	32
β-strand	57-61	5	32
β-strand	74-76	3	33
β-strand	85	1	33
α-helix	88-90	3
α-helix	94-97	4
β-strand	100-105	6	33
β-strand	108-110	3	33
α-helix	112-117	6
β-strand	123-128	6	33

Chain AH: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	37
β-strand	10	1	37
β-strand	15-22	8	37
β-strand	27-29	3	37
β-strand	32	1	37
α-helix	34-37	4
α-helix	44-47	4
α-helix	49-52	4
β-strand	60-67	8	37
α-helix	71-84	14
α-helix	91-93	3
α-helix	95-98	4
α-helix	109-113	5
α-helix	123-125	3

44 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
Small ribosomal subunit protein uS2	AA	protein	241	Escherichia coli	P0A7V0 (AlphaFold model)
Small ribosomal subunit protein uS3	AB	protein	233	Escherichia coli	P0A7V3 (AlphaFold model)
Small ribosomal subunit protein uS4	AC	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
Small ribosomal subunit protein uS5	AD	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
Small ribosomal subunit protein bS6, fully modified isoform	AE	protein	135	Escherichia coli	P02358
Small ribosomal subunit protein uS7	AF	protein	179	Escherichia coli	P02359
Small ribosomal subunit protein uS8	AG	protein	130	Escherichia coli	P0A7W7
Small ribosomal subunit protein uS9	AH	protein	130	Escherichia coli	P0A7X3
Small ribosomal subunit protein uS10	AI	protein	103	Escherichia coli	P0A7R5
Small ribosomal subunit protein uS11	AJ	protein	129	Escherichia coli	P0A7R9
Small ribosomal subunit protein uS12	AK	protein	124	Escherichia coli	P0A7S3
Small ribosomal subunit protein uS13	AL	protein	118	Escherichia coli	P0A7S9

42 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>9SS6_1 Small ribosomal subunit protein uS2 (chains AA)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 2 (AB), FASTA

>9SS6_2 Small ribosomal subunit protein uS3 (chains AB)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 3 (AC), FASTA

>9SS6_3 Small ribosomal subunit protein uS4 (chains AC)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 4 (AD), FASTA

>9SS6_4 Small ribosomal subunit protein uS5 (chains AD)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 5 (AE), FASTA

>9SS6_5 Small ribosomal subunit protein bS6, fully modified isoform (chains AE)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 6 (AF), FASTA

>9SS6_6 Small ribosomal subunit protein uS7 (chains AF)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 7 (AG), FASTA

>9SS6_7 Small ribosomal subunit protein uS8 (chains AG)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 8 (AH), FASTA

>9SS6_8 Small ribosomal subunit protein uS9 (chains AH)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 9 (AI), FASTA

>9SS6_9 Small ribosomal subunit protein uS10 (chains AI)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 10 (AJ), FASTA

>9SS6_10 Small ribosomal subunit protein uS11 (chains AJ)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV

Sequence of entity 11 (AK), FASTA

>9SS6_11 Small ribosomal subunit protein uS12 (chains AK)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Sequence of entity 12 (AL), FASTA

>9SS6_12 Small ribosomal subunit protein uS13 (chains AL)
MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEV
AKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK

Primary citation

Mechanistic insights into E. coli recovery from growth arrest. Hassan, A.H., Nakano, Y., Gamper, H. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-71781-6 · 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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