5NP6 | pdb_00005np6

70S structure prior to bypassing

PDB DOI: https://doi.org/10.2210/pdb5NP6/pdb
NAKB: 5NP6
EM Map EMD-3618: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Escherichia coli K-12, Tequatrovirus T4, Escherichia coli
Mutation(s): No

Deposited: 2017-04-13 Released: 2017-06-14
Deposition Author(s): Agirrezabala, X., Samatova, E., Klimova, M., Zamora, M., Gil-Carton, D., Rodnina, M., Valle, M.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness, German Research Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Ribosome rearrangements at the onset of translational bypassing.

Agirrezabala, X., Samatova, E., Klimova, M., Zamora, M., Gil-Carton, D., Rodnina, M.V., Valle, M.

(2017) Sci Adv 3: e1700147-e1700147

PubMed: 28630923 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.1700147
Primary Citation Related Structures:
5NP6

PubMed Abstract:
Bypassing is a recoding event that leads to the translation of two distal open reading frames into a single polypeptide chain. We present the structure of a translating ribosome stalled at the bypassing take-off site of gene 60 of bacteriophage T4. The nascent peptide in the exit tunnel anchors the P-site peptidyl-tRNA ^Gly to the ribosome and locks an inactive conformation of the peptidyl transferase center (PTC). The mRNA forms a short dynamic hairpin in the decoding site. The ribosomal subunits adopt a rolling conformation in which the rotation of the small subunit around its long axis causes the opening of the A-site region. Together, PTC conformation and mRNA structure safeguard against premature termination and read-through of the stop codon and reconfigure the ribosome to a state poised for take-off and sliding along the noncoding mRNA gap.

Organizational Affiliation

Structural Biology Unit, CIC bioGUNE, 48160 Derio, Spain.

Macromolecule Content

Total Structure Weight: 2,180.31 kDa
Atom Count: 146,883
Modeled Residue Count: 10,662
Deposited Residue Count: 10,662
Unique protein chains: 52
Unique nucleic acid chains: 5

Macromolecules

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase small subunit	C	46	Tequatrovirus T4	Mutation(s): 0 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P23992 (Enterobacteria phage T4) Explore P23992 Go to UniProtKB: P23992
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23992
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	E	218	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7V0
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	F	206	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7V3
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	G	205	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7V8 (Escherichia coli (strain K12)) Explore P0A7V8 Go to UniProtKB: P0A7V8
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7V8
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	H	157	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7W1
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	I	100	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P02358 (Escherichia coli (strain K12)) Explore P02358 Go to UniProtKB: P02358
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02358
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	J	151	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02359
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	K	129	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7W7 (Escherichia coli (strain K12)) Explore P0A7W7 Go to UniProtKB: P0A7W7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7W7
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	L	127	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7X3
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	M	98	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7R5
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	N	116	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7R9
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	O	123	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7S3
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	P	114	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7S9
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	Q	101	Escherichia coli K-12	Mutation(s): 0
UniProt
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: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	R	88	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0ADZ4 (Escherichia coli (strain K12)) Explore P0ADZ4 Go to UniProtKB: P0ADZ4
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UniProt Group	P0ADZ4
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	S	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7T3
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	T	80	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: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	U	65	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7T7
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	V	79	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: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	W	85	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: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S21	X	65	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P68679 (Escherichia coli (strain K12)) Explore P68679 Go to UniProtKB: P68679
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UniProt Group	P68679
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	AA [auth a]	271	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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UniProt Group	P60422
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	BA [auth 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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UniProt Group	P60438
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	CA [auth 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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UniProt Group	P60723
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	DA [auth d]	177	Escherichia coli K-12	Mutation(s): 0
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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: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	EA [auth e]	176	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: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	FA [auth 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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UniProt Group	P0A7R1
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	GA [auth g]	141	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7J7 (Escherichia coli (strain K12)) Explore P0A7J7 Go to UniProtKB: P0A7J7
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UniProt Group	P0A7J7
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	HA [auth h]	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: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	IA [auth i]	122	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: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	JA [auth j]	143	Escherichia coli K-12	Mutation(s): 0
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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: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	KA [auth k]	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: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	LA [auth l]	120	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: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	MA [auth m]	116	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: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	NA [auth n]	114	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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UniProt Group	P0A7K6
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	OA [auth o]	117	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: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	PA [auth p]	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: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	QA [auth q]	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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UniProt Group	P61175
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	RA [auth r]	93	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: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	SA [auth s]	102	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: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	TA [auth t]	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: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	UA [auth u]	75	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: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	VA [auth v]	77	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: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	WA [auth w]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7M6
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	XA [auth x]	58	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: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	YA [auth y]	56	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: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	ZA [auth z]	50	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: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	AB [auth 0]	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: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	BB [auth 1]	64	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: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	CB [auth 2]	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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Reference Sequence

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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L10	DB [auth 3]	131	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7J3 (Escherichia coli (strain K12)) Explore P0A7J3 Go to UniProtKB: P0A7J3
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UniProt Group	P0A7J3
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Reference Sequence

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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	EB [auth 4]	66	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12)) Explore P0A7M9 Go to UniProtKB: P0A7M9
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7M9
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