7QGH | pdb_00007qgh

Structure of the E. coli disome - collided 70S ribosome

PDB DOI: https://doi.org/10.2210/pdb7QGH/pdb
EM Map EMD-13955: EMDB EMDataResource
NAKB: 7QGH

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

Deposited: 2021-12-08 Released: 2022-03-16
Deposition Author(s): Kratzat, H., Buschauer, R., Berninghausen, O., Beckmann, R.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.48 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria.

Saito, K., Kratzat, H., Campbell, A., Buschauer, R., Burroughs, A.M., Berninghausen, O., Aravind, L., Green, R., Beckmann, R., Buskirk, A.R.

(2022) Nature 603: 503-508

PubMed: 35264790 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-022-04416-7
Primary Citation Related Structures:
7QG8, 7QGH, 7QGN, 7QGR, 7QGU, 7QH4

PubMed Abstract:
Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation ^1,2. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes ^3-6. Here, using a genetic screen in Escherichia coli, we discovered a new rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNAs ³) to rescue upstream ribosomes. SmrB is recruited to ribosomes and is activated by collisions. Cryo-electron microscopy structures of collided disomes from E. coli and Bacillus subtilis show distinct and conserved arrangements of individual ribosomes and the composite SmrB-binding site. These findings reveal the underlying mechanisms by which ribosome collisions trigger ribosome rescue in bacteria.

Organizational Affiliation

Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA.

Macromolecule Content

Total Structure Weight: 2,511.57 kDa
Atom Count: 147,973
Modeled Residue Count: 10,762
Deposited Residue Count: 12,273
Unique protein chains: 52
Unique nucleic acid chains: 6

Macromolecules

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	B [auth P]	275	Escherichia coli K-12	Mutation(s): 0

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	C [auth Q]	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	D [auth R]	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	E [auth S]	179	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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	F [auth T]	177	Escherichia coli K-12	Mutation(s): 0
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UniProt Group	P0AG55
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	G [auth V]	142	Escherichia coli K-12	Mutation(s): 0
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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: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	H [auth W]	142	Escherichia coli K-12	Mutation(s): 0
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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: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	I [auth X]	123	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0ADY3 (Escherichia coli (strain K12)) Explore P0ADY3 Go to UniProtKB: P0ADY3
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	J [auth Y]	144	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: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	K [auth Z]	137	Escherichia coli K-12	Mutation(s): 0

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	L [auth a]	127	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0AG44 (Escherichia coli (strain K12)) Explore P0AG44 Go to UniProtKB: P0AG44
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	M [auth b]	117	Escherichia coli K-12	Mutation(s): 0
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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: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	N [auth c]	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: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	O [auth d]	118	Escherichia coli K-12	Mutation(s): 0
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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: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	P [auth e]	103	Escherichia coli K-12	Mutation(s): 0
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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: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	Q [auth f]	110	Escherichia coli K-12	Mutation(s): 0
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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: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	R [auth g]	100	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Explore P0ADZ0 Go to UniProtKB: P0ADZ0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	S [auth h]	104	Escherichia coli K-12	Mutation(s): 0
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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: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	T [auth i]	94	Escherichia coli K-12	Mutation(s): 0
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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: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	U [auth j]	85	Escherichia coli K-12	Mutation(s): 0
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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: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	V [auth k]	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: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	W [auth l]	63	Escherichia coli K-12	Mutation(s): 0
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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: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	X [auth m]	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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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	Y [auth n]	57	Escherichia coli K-12	Mutation(s): 0
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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: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	Z [auth o]	55	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0A7N9 (Escherichia coli (strain K12)) Explore P0A7N9 Go to UniProtKB: P0A7N9
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	AA [auth p]	47	Escherichia coli K-12	Mutation(s): 0

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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	BA [auth q]	67	Escherichia coli K-12	Mutation(s): 0

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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	CA [auth r]	55	Escherichia coli K-12	Mutation(s): 0

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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	EA [auth L]	70	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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UniProt Group	P0A7M9
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L1	FA [auth C]	223	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A7L0 (Escherichia coli (strain K12)) Explore P0A7L0 Go to UniProtKB: P0A7L0
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UniProt Group	P0A7L0
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	GA [auth U]	149	Escherichia coli K-12	Mutation(s): 0
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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: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	KA [auth 1]	244	Escherichia coli K-12	Mutation(s): 0

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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	LA [auth 2]	237	Escherichia coli K-12	Mutation(s): 0

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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	MA [auth 3]	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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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	NA [auth 4]	162	Escherichia coli K-12	Mutation(s): 0
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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: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6, non-modified isoform	OA [auth 5]	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: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	PA [auth 6]	152	Escherichia coli K-12	Mutation(s): 0
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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: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	QA [auth 7]	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: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	RA [auth 8]	130	Escherichia coli K-12	Mutation(s): 0
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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: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	SA [auth 9]	110	Escherichia coli K-12	Mutation(s): 0

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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	TA [auth A]	129	Escherichia coli K-12	Mutation(s): 0
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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: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	UA [auth B]	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: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	VA [auth D]	118	Escherichia coli K-12	Mutation(s): 0
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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: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	WA [auth E]	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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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	XA [auth F]	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: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	YA [auth G]	100	Escherichia coli K-12	Mutation(s): 0

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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	ZA [auth H]	84	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0AG63 (Escherichia coli (strain K12)) Explore P0AG63 Go to UniProtKB: P0AG63
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	AB [auth I]	75	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0A7T7 (Escherichia coli (strain K12)) Explore P0A7T7 Go to UniProtKB: P0A7T7
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	BB [auth J]	92	Escherichia coli K-12	Mutation(s): 0

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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	CB [auth K]	87	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0A7U7 (Escherichia coli (strain K12)) Explore P0A7U7 Go to UniProtKB: P0A7U7
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S21	DB [auth s]	88	Escherichia coli K-12	Mutation(s): 0

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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S1	EB [auth t]	557	Escherichia coli K-12	Mutation(s): 0
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Find proteins for P0AG67 (Escherichia coli (strain K12)) Explore P0AG67 Go to UniProtKB: P0AG67
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