9RTV image
Deposition Date 2025-07-03
Release Date 2025-10-29
Last Version Date 2025-11-12
Entry Detail
PDB ID:
9RTV
Keywords:
RIBOSOME
Title:
Structure of the 70S-EF-G(P610L)-GDP-Pi ribosome complex with tRNAs in hybrid state 2 (H2-EF-G(P610L)-GDP-Pi)
Biological Source:
Source Organism:
Escherichia coli K-12 (Taxon ID: 83333)
Host Organism:
Escherichia coli K-12
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9RTV validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:A (auth: 0)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7N4 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33
Gene (Uniprot):rpmG
Chain IDs:B (auth: 1)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7N9 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34
Gene (Uniprot):rpmH
Chain IDs:C (auth: 2)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7P5 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:D (auth: 3)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7Q1 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:E (auth: 4)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7Q6 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:F (auth: 5)
Chain Length:165
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7J3 Pfam ID:PF00466
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:G (auth: 6)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7M9 Pfam ID:PF01197
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:H (auth: A)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:I (auth: B)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli K-12
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:J (auth: C)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:K (auth: D)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60438 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:L (auth: E)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60723 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:M (auth: F)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P62399 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:N (auth: G)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG55 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:O (auth: H)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:P (auth: I)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:Q (auth: J)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AA10 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:R (auth: K)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADY3 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:S (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P02413 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:T (auth: M)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADY7 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:U (auth: N)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG44 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:V (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0C018 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:W (auth: P)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7K6 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:X (auth: Q)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7L3 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:Y (auth: R)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG48 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:Z (auth: S)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P61175 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:AA (auth: T)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADZ0 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:BA (auth: U)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:CA (auth: V)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P68919 Pfam ID:PF01386
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Gene (Uniprot):rpmA
Chain IDs:DA (auth: W)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7L8 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:EA (auth: X)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7M2 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:FA (auth: Y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7M6 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:GA (auth: Z)
Chain Length:33
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG51 Pfam ID:PF00327
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:HA (auth: a)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli K-12
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:IA (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7V0 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rpsC
Chain IDs:JA (auth: c)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:C3SQX2 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Gene (Uniprot):rpsD
Chain IDs:KA (auth: d)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:C4ZUF1 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:LA (auth: e)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:MA (auth: f)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P02358 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:NA (auth: g)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P02359 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:OA (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7W7 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:PA (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7X3 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:QA (auth: j)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7R5 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:RA (auth: k)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7R9 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:SA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7S3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:TA (auth: m)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7S9 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:UA (auth: n)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG59 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rpsO
Chain IDs:VA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADZ4 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:WA (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7T3 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:XA (auth: q)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG63 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:YA (auth: r)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7T7 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:ZA (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7U3 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:AB (auth: t)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7U7 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:BB (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P68679 Pfam ID:PF01165
Polymer Type:polyribonucleotide
Molecule:P/E-site tRNA(fMet)
Chain IDs:CB (auth: v)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:A/P-site tRNA(Phe)
Chain IDs:DB (auth: w)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli K-12
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Elongation factor G
Gene (Uniprot):fusA
Chain IDs:EB (auth: x)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:C4ZUJ5 Pfam ID:PF00009, PF03144, PF14492, PF03764, PF00679
Polymer Type:polypeptide(L)
Molecule:Dipeptide (FME-PHE)
Chain IDs:FB (auth: y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:GB (auth: z)
Chain Length:33
Number of Molecules:1
Biological Source:Escherichia coli K-12
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG HA G modified residue
4OC HA C modified residue
4SU CB U modified residue
5MC HA C modified residue
5MU CB U modified residue
G7M HA G modified residue
H2U CB U modified residue
MA6 HA A modified residue
PSU HA U modified residue
UR3 HA U modified residue
Ligand Molecules
AM2
GDP
MG
NA
PO4
ZN
Primary Citation
Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides.
Nat Commun 16 9568 9568 (2025)
PMID: 41162373 DOI: 10.1038/s41467-025-65298-7

Abstact

Antibiotic resistance is a growing threat, underscoring the need to understand the underlying mechanisms. Aminoglycosides kill bacteria by disrupting translation fidelity, leading to the synthesis of aberrant proteins. Surprisingly, mutations in fusA, a gene encoding translation elongation factor G (EF-G), frequently confer resistance, even though EF-G neither participates in mRNA decoding nor blocks aminoglycoside binding. Here, we show that EF-G resistance variants selectively slow ribosome movement along mRNA when aminoglycosides are bound. This delay increases the chance that the drug dissociates before misreading occurs. Over several elongation cycles, this selective silencing of drug-bound ribosomes prevents error cluster formation, preserving proteome and membrane integrity. As a result, fusA mutations confer resistance early in treatment by preventing self-promoted aminoglycoside uptake. Translation on drug-free ribosomes remains sufficiently rapid to sustain near-normal bacterial growth. The mechanism of selective silencing of corrupted targets reveals a previously unrecognized antibiotic resistance strategy with potential therapeutic implications.

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Protein

Chemical

Disease

Primary Citation of related structures
9RTV
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