8QOA: SecM-stalled Escherichia coli 70S ribosome

Name: PDB 8QOA: Structure of SecM-stalled Escherichia coli 70S ribosome
Published: 2024-03-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of SecM-stalled Escherichia coli 70S ribosome. Determined by electron microscopy at 2.0 Å resolution. Released 20 Mar 2024.

Method: Electron microscopy
Resolution: 2.0 Å
Organism: Escherichia coli BW25113
Chains: 57
Atoms: 147,750
Mol. weight: 2209.39 kDa
Ligands: ZN, MG, PRO
Released: 20 Mar 2024

Explore 8QOA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QOA contains 267 α-helices and 302 β-strands across 50 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	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 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	16
β-strand	22-24	3	16
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	16
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	19
β-strand	14-19	6	19
β-strand	22-27	6	19
α-helix	31-33	3
β-strand	35-37	3	19

Chain 4: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	10-16	7	93
β-strand	21-26	6	93
α-helix	31	1
β-strand	32-34	3	93
α-helix	42-45	4
α-helix	56-63	8

Chain 6: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	152-158	7

Chain B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16	1	32
α-helix	20-22	3
α-helix	25-30	6
β-strand	31-34	4	32
β-strand	39-41	3	32
α-helix	43-62	20
β-strand	67-70	4	33
α-helix	77-86	10
β-strand	90-92	3	33
α-helix	104-123	20
α-helix	125-128	4
α-helix	131-148	18
β-strand	160-163	4	33
α-helix	170-179	10
β-strand	183-187	5	33
β-strand	198-201	4	33
α-helix	207-226	20

Chain c: 8 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	2
α-helix	6-7	2
β-strand	17-19	3	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	6
β-strand	76-82	7	6
β-strand	91-96	6	6
β-strand	101-105	5	6
β-strand	107	1	7
β-strand	115-116	2	6
β-strand	118	1	8
β-strand	129-131	3	8
α-helix	136	1
β-strand	140-142	3	8
β-strand	144-145	2	9
β-strand	152-154	3	9
β-strand	162-168	7	8
β-strand	171-175	5	8
β-strand	181-185	5	8
β-strand	189-192	4	8
β-strand	195	1	7
α-helix	198-202	5
β-strand	204	1	2
α-helix	208-213	6
β-strand	216	1	5
α-helix	217-221	5
α-helix	222-224	3
β-strand	245	1	10
β-strand	251	1	10
α-helix	264-266	3
β-strand	267-269	3	8

42 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
Large ribosomal subunit protein bL33	0	protein	55	Escherichia coli BW25113	P0A7N9 (AlphaFold model)
Large ribosomal subunit protein bL34	1	protein	46	Escherichia coli BW25113	P0A7P5 (AlphaFold model)
Large ribosomal subunit protein bL35	2	protein	65	Escherichia coli BW25113	P0A7Q1 (AlphaFold model)
Large ribosomal subunit protein bL36A	3	protein	38	Escherichia coli BW25113	P0A7Q6 (AlphaFold model)
E-site tRNA	5	RNA	2	Escherichia coli BW25113
30S ribosomal protein S2	B	protein	241	Escherichia coli BW25113	P0A7V0
Small ribosomal subunit protein uS3	C	protein	233	Escherichia coli BW25113	P0A7V3
Small ribosomal subunit protein uS4	D	protein	206	Escherichia coli BW25113	P0A7V8
Small ribosomal subunit protein uS5	E	protein	167	Escherichia coli BW25113	P0A7W1
30S ribosomal protein S6, fully modified isoform	F	protein	135	Escherichia coli BW25113	P02358
30S ribosomal protein S7	G	protein	179	Escherichia coli BW25113	P02359
Small ribosomal subunit protein uS8	H	protein	130	Escherichia coli BW25113	P0A7W7

45 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8QOA_1 Large ribosomal subunit protein bL33 (chains 0)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK

Sequence of entity 2 (1), FASTA

>8QOA_2 Large ribosomal subunit protein bL34 (chains 1)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Sequence of entity 3 (2), FASTA

>8QOA_3 Large ribosomal subunit protein bL35 (chains 2)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA

Sequence of entity 4 (3), FASTA

>8QOA_4 Large ribosomal subunit protein bL36A (chains 3)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG

Sequence of entity 5 (5), FASTA

>8QOA_5 E-site tRNA (chains 5)
CA

Sequence of entity 6 (B), FASTA

>8QOA_6 30S ribosomal protein S2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 7 (C), FASTA

>8QOA_7 Small ribosomal subunit protein uS3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 8 (D), FASTA

>8QOA_8 Small ribosomal subunit protein uS4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 9 (E), FASTA

>8QOA_9 Small ribosomal subunit protein uS5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 10 (F), FASTA

>8QOA_10 30S ribosomal protein S6, fully modified isoform (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 11 (G), FASTA

>8QOA_11 30S ribosomal protein S7 (chains G)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 12 (H), FASTA

>8QOA_12 Small ribosomal subunit protein uS8 (chains H)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	288
PRO	Proline	C5 H9 N O2	1

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

Primary citation

The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome. Gersteuer, F., Morici, M., Gabrielli, S. et al. Nat Commun (2024) 15:2431-2431. DOI 10.1038/s41467-024-46762-2 · PubMed

Other PDB entries of the same protein (UniProt P0A7N9 (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…
8CGK 1.64 Å, Lincomycin and Avilamycin bound to the 50S subunit
8CGV 1.66 Å, Tiamulin bound to the 50S subunit
8CEU 1.83 Å, Retapamulin and Capreomycin bound to the 50S subunit
8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
8CAM 1.86 Å, Evernimicin bound to the 50S subunit
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
9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain
9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
9D89 1.95 Å, E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)

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