9H0L image
Deposition Date 2024-10-08
Release Date 2025-05-28
Last Version Date 2025-07-09
Entry Detail
PDB ID:
9H0L
Keywords:
RIBOSOME
Title:
70S ribosome with cognate tRNASer3 bound to A-site AGC codon
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.49 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9H0L validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33
Gene (Uniprot):rpmG
Chain IDs:ZA (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7N9 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34
Gene (Uniprot):rpmH
Chain IDs:AB (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7P5 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35
Gene (Uniprot):rpmI
Chain IDs:BB (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q1 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL36A
Gene (Uniprot):rpmJ
Chain IDs:CB (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q6 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL31A
Gene (Uniprot):rpmE
Chain IDs:DB (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M9 Pfam ID:PF01197
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
Gene (Uniprot):rpsB
Chain IDs:B
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V0 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rpsC
Chain IDs:C
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Gene (Uniprot):rpsD
Chain IDs:D
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rpsE
Chain IDs:E
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS6, fully modified isoform
Gene (Uniprot):rpsF
Chain IDs:F
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02358 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):rpsG
Chain IDs:G
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02359 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rpsH
Chain IDs:H
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7W7 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rpsI
Chain IDs:I
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7X3 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):rpsJ
Chain IDs:J
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R5 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
Gene (Uniprot):rpsK
Chain IDs:K
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R9 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rpsL
Chain IDs:L
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7S3 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Gene (Uniprot):rpsM
Chain IDs:M
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7S9 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Gene (Uniprot):rpsN
Chain IDs:N
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG59 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rpsO
Chain IDs:O
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADZ4 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS16
Gene (Uniprot):rpsP
Chain IDs:P
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7T3 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rpsQ
Chain IDs:Q
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG63 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS18
Gene (Uniprot):rpsR
Chain IDs:R
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7T7 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):rpsS
Chain IDs:S
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7U3 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS20
Gene (Uniprot):rpsT
Chain IDs:T
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7U7 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS21
Gene (Uniprot):rpsU
Chain IDs:U
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P68679 Pfam ID:PF01165
Polymer Type:polyribonucleotide
Molecule:tRNA(fMet)
Chain IDs:V, Y (auth: Z)
Chain Length:85
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:W (auth: X)
Chain Length:24
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA(Ser3)
Chain IDs:X (auth: Y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:Z (auth: a)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:AA (auth: b)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rplB
Chain IDs:BA (auth: c)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Gene (Uniprot):rplC
Chain IDs:CA (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60438 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
Gene (Uniprot):rplD
Chain IDs:DA (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60723 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
Gene (Uniprot):rplE
Chain IDs:EA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P62399 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Gene (Uniprot):rplF
Chain IDs:FA (auth: g)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG55 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL9
Gene (Uniprot):rplI
Chain IDs:GA (auth: h)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rplM
Chain IDs:HA (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AA10 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
Gene (Uniprot):rplN
Chain IDs:IA (auth: j)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY3 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
Gene (Uniprot):rplO
Chain IDs:JA (auth: k)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02413 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16
Gene (Uniprot):rplP
Chain IDs:KA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY7 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17
Gene (Uniprot):rplQ
Chain IDs:LA (auth: m)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG44 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rplR
Chain IDs:MA (auth: n)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0C018 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL19
Gene (Uniprot):rplS
Chain IDs:NA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7K6 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20
Gene (Uniprot):rplT
Chain IDs:OA (auth: p)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L3 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21
Gene (Uniprot):rplU
Chain IDs:PA (auth: q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG48 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Gene (Uniprot):rplV
Chain IDs:QA (auth: r)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P61175 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rplW
Chain IDs:RA (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADZ0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Gene (Uniprot):rplX
Chain IDs:SA (auth: t)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL25
Gene (Uniprot):rplY
Chain IDs:TA (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P68919 Pfam ID:PF01386
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Gene (Uniprot):rpmA
Chain IDs:UA (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L8 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28
Gene (Uniprot):rpmB
Chain IDs:VA (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M2 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpmC
Chain IDs:WA (auth: x)
Chain Length:24
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M6 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpmD
Chain IDs:XA (auth: y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG51 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32
Gene (Uniprot):rpmF
Chain IDs:YA (auth: z)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7N4 Pfam ID:PF01783
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG A G modified residue
4D4 KA ARG modified residue
4OC A C modified residue
4SU X U modified residue
5MC A C modified residue
5MU X U modified residue
D2T L ASP modified residue
G7M A G modified residue
H2U X U modified residue
MA6 A A modified residue
MEQ CA GLN modified residue
PSU A U modified residue
RSP X C modified residue
T6A X A modified residue
UR3 A U modified residue
Ligand Molecules
MG
PUT
SPD
SPM
ZN
Primary Citation
Doublet decoding of tRNA Ser3 demonstrates plasticity of ribosomal decoding center.
Nat Commun 16 5402 5402 (2025)
PMID: 40571681 DOI: 10.1038/s41467-025-61016-5

Abstact

Frameshifts can be caused by specific combinations of tRNA and mRNA. The wildtype AGC-decoding E. coli tRNASer3GCU has been shown to induce -1 ribosomal frameshifting on GCA alanine codons, and proposed to read a two-base codon instead of a canonical triplet. However, it has remained unclear whether this type of non-cognate decoding can be accommodated by the ribosome. Here, we perform single-particle cryo-EM reconstructions on E. coli 70S ribosomes with the frameshift-inducing tRNASer3 bound to the non-cognate GCA codon or the cognate AGC codon in the ribosomal A site. The structures demonstrate that doublet decoding is made possible when A1493, the conserved monitoring base in 16S rRNA, mimics a first codon base, forming a Hoogsteen base pair with U36 from the anticodon and stacking with the mRNA. This interaction pushes the first two bases of the A-site codon in position for base pairing with C35 and G34 of the anticodon.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
9GXX