8BHJ | pdb_00008bhj

Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and Am6AA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site

PDB DOI: https://doi.org/10.2210/pdb8BHJ/pdb
EM Map EMD-16057: EMDB EMDataResource
NAKB: 8BHJ

Classification: TRANSLATION
Organism(s): Escherichia coli K-12, synthetic construct
Mutation(s): No

Deposited: 2022-10-31 Released: 2023-08-16
Deposition Author(s): Koziej, L., Glatt, S.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.81 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Modulation of translational decoding by m 6 A modification of mRNA.

Jain, S., Koziej, L., Poulis, P., Kaczmarczyk, I., Gaik, M., Rawski, M., Ranjan, N., Glatt, S., Rodnina, M.V.

(2023) Nat Commun 14: 4784-4784

PubMed: 37553384 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-40422-7
Primary Citation Related Structures:
8BF7, 8BGE, 8BGH, 8BH4, 8BHJ, 8BHL, 8BHN, 8BHP, 8BIL, 8BIM

PubMed Abstract:
N ⁶-methyladenosine (m ⁶A) is an abundant, dynamic mRNA modification that regulates key steps of cellular mRNA metabolism. m ⁶A in the mRNA coding regions inhibits translation elongation. Here, we show how m ⁶A modulates decoding in the bacterial translation system using a combination of rapid kinetics, smFRET and single-particle cryo-EM. We show that, while the modification does not impair the initial binding of aminoacyl-tRNA to the ribosome, in the presence of m ⁶A fewer ribosomes complete the decoding process due to the lower stability of the complexes and enhanced tRNA drop-off. The mRNA codon adopts a π-stacked codon conformation that is remodeled upon aminoacyl-tRNA binding. m ⁶A does not exclude canonical codon-anticodon geometry, but favors alternative more dynamic conformations that are rejected by the ribosome. These results highlight how modifications outside the Watson-Crick edge can still interfere with codon-anticodon base pairing and complex recognition by the ribosome, thereby modulating the translational efficiency of modified mRNAs.

Organizational Affiliation

Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany.

Macromolecule Content

Total Structure Weight: 2,191.15 kDa
Atom Count: 142,196
Modeled Residue Count: 10,198
Deposited Residue Count: 10,590
Unique protein chains: 49
Unique nucleic acid chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	A	273	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P60422 (Escherichia coli (strain K12)) Explore P60422 Go to UniProtKB: P60422
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60422
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	B	209	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P60438 (Escherichia coli (strain K12)) Explore P60438 Go to UniProtKB: P60438
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60438
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	C	201	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P60723 (Escherichia coli (strain K12)) Explore P60723 Go to UniProtKB: P60723
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60723
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	D	179	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P62399 (Escherichia coli (strain K12)) Explore P62399 Go to UniProtKB: P62399
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UniProt Group	P62399
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	E	177	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12)) Explore P0AG55 Go to UniProtKB: P0AG55
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UniProt Group	P0AG55
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	F	149	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12)) Explore P0A7R1 Go to UniProtKB: P0A7R1
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7R1
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	G	142	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12)) Explore P0AA10 Go to UniProtKB: P0AA10
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UniProt Group	P0AA10
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	H	123	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12)) Explore P0ADY3 Go to UniProtKB: P0ADY3
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UniProt Group	P0ADY3
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	I	144	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P02413 (Escherichia coli (strain K12)) Explore P02413 Go to UniProtKB: P02413
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UniProt Group	P02413
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	J	136	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12)) Explore P0ADY7 Go to UniProtKB: P0ADY7
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UniProt Group	P0ADY7
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	K	127	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12)) Explore P0AG44 Go to UniProtKB: P0AG44
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UniProt Group	P0AG44
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	L	117	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12)) Explore P0C018 Go to UniProtKB: P0C018
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UniProt Group	P0C018
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	M	115	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Explore P0A7K6 Go to UniProtKB: P0A7K6
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7K6
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	N	118	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12)) Explore P0A7L3 Go to UniProtKB: P0A7L3
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UniProt Group	P0A7L3
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	O	103	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12)) Explore P0AG48 Go to UniProtKB: P0AG48
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UniProt Group	P0AG48
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	P	110	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P61175 (Escherichia coli (strain K12)) Explore P61175 Go to UniProtKB: P61175
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61175
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	Q	100	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Explore P0ADZ0 Go to UniProtKB: P0ADZ0
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UniProt Group	P0ADZ0
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	R	104	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P60624 (Escherichia coli (strain K12)) Explore P60624 Go to UniProtKB: P60624
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UniProt Group	P60624
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	S	94	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P68919 (Escherichia coli (strain K12)) Explore P68919 Go to UniProtKB: P68919
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UniProt Group	P68919
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	T	85	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Explore P0A7L8 Go to UniProtKB: P0A7L8
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UniProt Group	P0A7L8
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	U	78	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12)) Explore P0A7M2 Go to UniProtKB: P0A7M2
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UniProt Group	P0A7M2
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	V	63	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12)) Explore P0A7M6 Go to UniProtKB: P0A7M6
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UniProt Group	P0A7M6
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	W	59	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0AG51 (Escherichia coli (strain K12)) Explore P0AG51 Go to UniProtKB: P0AG51
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UniProt Group	P0AG51
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	X [auth a]	57	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Explore P0A7N4 Go to UniProtKB: P0A7N4
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UniProt Group	P0A7N4
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	Y [auth b]	55	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12)) Explore P0A7N9 Go to UniProtKB: P0A7N9
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UniProt Group	P0A7N9
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	Z [auth c]	46	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12)) Explore P0A7P5 Go to UniProtKB: P0A7P5
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UniProt Group	P0A7P5
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	AA [auth d]	65	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12)) Explore P0A7Q1 Go to UniProtKB: P0A7Q1
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UniProt Group	P0A7Q1
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	BA [auth e]	38	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12)) Explore P0A7Q6 Go to UniProtKB: P0A7Q6
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UniProt Group	P0A7Q6
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	CA [auth f]	241	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7V0 (Escherichia coli (strain K12)) Explore P0A7V0 Go to UniProtKB: P0A7V0
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UniProt Group	P0A7V0
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	DA [auth g]	233	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12)) Explore P0A7V3 Go to UniProtKB: P0A7V3
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UniProt Group	P0A7V3
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	EA [auth h]	206	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0A7V8 (Escherichia coli (strain K12)) Explore P0A7V8 Go to UniProtKB: P0A7V8
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UniProt Group	P0A7V8
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	FA [auth i]	167	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7W1 (Escherichia coli (strain K12)) Explore P0A7W1 Go to UniProtKB: P0A7W1
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UniProt Group	P0A7W1
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	GA [auth j]	131	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P02358 (Escherichia coli (strain K12)) Explore P02358 Go to UniProtKB: P02358
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UniProt Group	P02358
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	HA [auth k]	179	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P02359 (Escherichia coli (strain K12)) Explore P02359 Go to UniProtKB: P02359
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UniProt Group	P02359
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	IA [auth l]	130	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0A7W7 (Escherichia coli (strain K12)) Explore P0A7W7 Go to UniProtKB: P0A7W7
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UniProt Group	P0A7W7
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	JA [auth m]	130	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7X3 (Escherichia coli (strain K12)) Explore P0A7X3 Go to UniProtKB: P0A7X3
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UniProt Group	P0A7X3
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	KA [auth n]	103	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7R5 (Escherichia coli (strain K12)) Explore P0A7R5 Go to UniProtKB: P0A7R5
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UniProt Group	P0A7R5
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	LA [auth o]	129	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12)) Explore P0A7R9 Go to UniProtKB: P0A7R9
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UniProt Group	P0A7R9
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	MA [auth p]	124	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12)) Explore P0A7S3 Go to UniProtKB: P0A7S3
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UniProt Group	P0A7S3
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	NA [auth q]	118	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7S9 (Escherichia coli (strain K12)) Explore P0A7S9 Go to UniProtKB: P0A7S9
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UniProt Group	P0A7S9
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	OA [auth r]	101	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0AG59 (Escherichia coli (strain K12)) Explore P0AG59 Go to UniProtKB: P0AG59
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UniProt Group	P0AG59
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	PA [auth s]	89	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0ADZ4 (Escherichia coli (strain K12)) Explore P0ADZ4 Go to UniProtKB: P0ADZ4
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	QA [auth t]	82	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12)) Explore P0A7T3 Go to UniProtKB: P0A7T3
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UniProt Group	P0A7T3
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	RA [auth u]	84	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12)) Explore P0AG63 Go to UniProtKB: P0AG63
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UniProt Group	P0AG63
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	SA [auth v]	75	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12)) Explore P0A7T7 Go to UniProtKB: P0A7T7
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UniProt Group	P0A7T7
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	TA [auth w]	92	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12)) Explore P0A7U3 Go to UniProtKB: P0A7U3
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UniProt Group	P0A7U3
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	UA [auth x]	87	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12)) Explore P0A7U7 Go to UniProtKB: P0A7U7
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UniProt Group	P0A7U7
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S21	VA [auth y]	71	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P68679 (Escherichia coli (strain K12)) Explore P68679 Go to UniProtKB: P68679
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68679
Sequence Annotations Expand
Reference Sequence