9SYH: E. coli 70S ribosome from deltaRlmE strain

Name: PDB 9SYH: E. coli 70S ribosome from deltaRlmE strain
Published: 2026-03-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

E. coli 70S ribosome from deltaRlmE strain. Determined by electron microscopy at 1.89 Å resolution. Released 18 Mar 2026.

Method: Electron microscopy
Resolution: 1.89 Å
Organism: Escherichia coli
Chains: 56
Atoms: 151,053
Mol. weight: 2270.12 kDa
Ligands: MG, SR0, PUT, ZN
Released: 18 Mar 2026

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

Secondary structure: helices and β-sheets

9SYH contains 252 α-helices and 309 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 0: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	96
β-strand	20-25	6	96
α-helix	33-34	2
β-strand	35-40	6	96
β-strand	45-53	9	96

Chain 1: 3 helices, 0 β-strands

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

Chain 2: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	8-11	4
β-strand	15-16	2	10
β-strand	22-24	3	10
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	10
α-helix	50-51	2
α-helix	52-61	10

Chain 3: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	17
β-strand	14-19	6	17
β-strand	22-27	6	17
α-helix	31-33	3
β-strand	35-37	3	17

Chain 4: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	10-16	7	23
β-strand	21-26	6	23
β-strand	32-34	3	23
α-helix	42-45	4
α-helix	56-63	8

Chain B: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
β-strand	16-19	4	11
α-helix	20-22	3
α-helix	25-27	3
β-strand	31-34	4	11
β-strand	38-41	4	11
α-helix	43-61	19
β-strand	68-70	3	12
α-helix	74-86	13
β-strand	90-92	3	12
α-helix	96-97	2
α-helix	104-122	19
α-helix	125-128	4
α-helix	133-148	16
α-helix	149-151	3
β-strand	163-164	2	12
α-helix	170-179	10
β-strand	184-187	4	12
β-strand	198-201	4	12
α-helix	207-225	19

Chain c: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
α-helix	6-7	2
β-strand	17-19	3	1
β-strand	24	1	2
α-helix	31-33	3
β-strand	34-36	3	3
β-strand	43	1	4
β-strand	49	1	4
β-strand	54	1	5
β-strand	61-63	3	3
β-strand	65	1	2
β-strand	76-82	7	2
β-strand	91-96	6	2
β-strand	101-105	5	2
β-strand	107	1	6
β-strand	115-116	2	2
β-strand	118	1	7
β-strand	129-131	3	7
α-helix	132-134	3
β-strand	140-142	3	7
β-strand	144-145	2	8
β-strand	152-154	3	8
β-strand	162-168	7	7
β-strand	171-175	5	7
β-strand	181-185	5	7
β-strand	189-192	4	7
β-strand	195	1	6
α-helix	198-202	5
β-strand	204	1	1
α-helix	208-213	6
β-strand	216	1	5
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	9
β-strand	251	1	9
α-helix	264-266	3
β-strand	267-269	3	7

Chain C: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	12	1	18
β-strand	16	1	18
β-strand	20-21	2	19
α-helix	26-46	21
β-strand	52-58	7	19
β-strand	64-70	7	19
α-helix	73-77	5
α-helix	83-95	13
β-strand	99-105	7	19
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-143	14
β-strand	148-155	8	20
α-helix	157-159	3
β-strand	164-171	8	20
β-strand	180-191	12	20
β-strand	194-206	13	20

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 rRNA	A	RNA	1542	Escherichia coli
Small ribosomal subunit protein uS2	B	protein	241	Escherichia coli	P0A7V0 (AlphaFold model)
Small ribosomal subunit protein uS3	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)
Small ribosomal subunit protein bS6, fully modified isoform	F	protein	135	Escherichia coli	P02358
Small ribosomal subunit protein uS7	G	protein	179	Escherichia coli	P02359
Small ribosomal subunit protein uS8	H	protein	130	Escherichia coli	P0A7W7
Small ribosomal subunit protein uS9	I	protein	130	Escherichia coli	P0A7X3
Small ribosomal subunit protein uS10	J	protein	103	Escherichia coli	P0A7R5
Small ribosomal subunit protein uS11	K	protein	129	Escherichia coli	P0A7R9
Small ribosomal subunit protein uS12	L	protein	124	Escherichia coli	P0A7S3

43 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9SYH_1 16S rRNA (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

>9SYH_2 Small ribosomal subunit protein uS2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (C), FASTA

>9SYH_3 Small ribosomal subunit protein uS3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (D), FASTA

>9SYH_4 Small ribosomal subunit protein uS4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (E), FASTA

>9SYH_5 Small ribosomal subunit protein uS5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (F), FASTA

>9SYH_6 Small ribosomal subunit protein bS6, fully modified isoform (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (G), FASTA

>9SYH_7 Small ribosomal subunit protein uS7 (chains G)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (H), FASTA

>9SYH_8 Small ribosomal subunit protein uS8 (chains H)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (I), FASTA

>9SYH_9 Small ribosomal subunit protein uS9 (chains I)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (J), FASTA

>9SYH_10 Small ribosomal subunit protein uS10 (chains J)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (K), FASTA

>9SYH_11 Small ribosomal subunit protein uS11 (chains K)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHDG
CRPPKKRRV

Sequence of entity 12 (L), FASTA

>9SYH_12 Small ribosomal subunit protein uS12 (chains L)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	351
SR0	N~1~-(3-azaniumylpropyl)butane-1,4-diaminium	C7 H22 N3	6
PUT	1,4-diaminobutane	C4 H12 N2	9
ZN	Zinc ion	Zn	2

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

Primary citation

23S rRNA modifications stimulate catalytic activity and prevent the formation of alternative structures. Larsson, D.S.D., Liiv, A., Ero, R. et al. Nucleic Acids Res (2026) 54. DOI 10.1093/nar/gkag800 · 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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