8UX8 image
Deposition Date 2023-11-09
Release Date 2025-07-09
Last Version Date 2025-08-27
Entry Detail
PDB ID:
8UX8
Keywords:
RIBOSOME
Title:
E. coli 70S ribosome with unmodified Lys-tRNAPro(GGG) bound to slippery P-site CCC-C codon in the +1 mRNA reading frame
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8UX8 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:A (auth: 1)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:B (auth: 2)
Chain Length:1540
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:C (auth: 3)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:D (auth: 4)
Chain Length:18
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:Lys-tRNA^proL
Chain IDs:E (auth: 5)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL1
Gene (Uniprot):rplA
Chain IDs:F (auth: A)
Chain Length:229
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A5P0JAY3 Pfam ID:PF00687
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:G (auth: B)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli
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:H (auth: C)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
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:I (auth: D)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A1AGK6 Pfam ID:PF00573
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:J (auth: E)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:K (auth: F)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SR17 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:L (auth: G)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SFP2 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rplM
Chain IDs:M (auth: J)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AA12 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:N (auth: K)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:S1NW45 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:O (auth: L)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A037Y8L6 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:P (auth: M)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
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:Q (auth: N)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SR72 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rplR
Chain IDs:R (auth: O)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A828U007 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL19
Gene (Uniprot):rplS
Chain IDs:S (auth: P)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7K8 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:T (auth: Q)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:B7MAS6 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:U (auth: R)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SSG2 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:V (auth: S)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
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:W (auth: T)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQV2 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:X (auth: U)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQZ7 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL25
Gene (Uniprot):rplY
Chain IDs:Y (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
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:Z (auth: W)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SSG7 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:AA (auth: X)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A1X3JA73 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpmC
Chain IDs:BA (auth: Y)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQY2 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:CA (auth: Z)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SR32 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:DA (auth: a)
Chain Length:229
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M9 Pfam ID:PF01197
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:EA (auth: b)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3TE02 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:FA (auth: c)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SME7 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:GA (auth: d)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:B7MGC4 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:HA (auth: e)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
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:IA (auth: f)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A0E2L017 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:JA (auth: g)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3TPN2 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:KA (auth: h)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:B7MCS9 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:LA (auth: i)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V8 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:MA (auth: j)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
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:NA (auth: k)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli
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:OA (auth: l)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02359 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rpsH
Chain IDs:PA (auth: m)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SR12 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rpsI
Chain IDs:QA (auth: n)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SRY2 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):rpsJ
Chain IDs:RA (auth: o)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQT7 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:SA (auth: p)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:B7MCR3 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rpsL
Chain IDs:TA (auth: q)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQR7 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:UA (auth: r)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A7U9IV78 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Gene (Uniprot):rpsN
Chain IDs:VA (auth: s)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A2X1PQW4 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:WA (auth: t)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SSQ7 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:XA (auth: u)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SYP2 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rpsQ
Chain IDs:YA (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQY7 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:ZA (auth: w)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A0E2KXL3 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):rpsS
Chain IDs:AB (auth: x)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQW2 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:BB (auth: y)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3TRH7 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:CB (auth: z)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A0E2L2J1 Pfam ID:PF01165
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
0TD TA ASP modified residue
2MG B G modified residue
4OC B C modified residue
5MC B C modified residue
7MG B G modified residue
MA6 B A modified residue
PSU B U modified residue
UR3 B U modified residue
Ligand Molecules
LYS
MG
Primary Citation
An RNA modification prevents extended codon-anticodon interactions from facilitating +1 frameshifting.
Nat Commun 16 7392 7392 (2025)
PMID: 40789848 DOI: 10.1038/s41467-025-62342-4

Abstact

RNA post-transcriptional modifications act by stabilizing the functional conformations of RNA. While their role in messenger RNA (mRNA) decoding is well established, it is less clear how transfer RNA (tRNA) modifications outside the anticodon contribute to tRNA stability and accurate protein synthesis. Absence of such modifications causes translation errors, including mRNA frameshifting. By integrating single-molecule fluorescence resonance energy transfer and cryogenic electron microscopy, we demonstrate that the N1-methylguanosine (m1G) modification at position 37 of Escherichia coli tRNAProL is necessary and sufficient for modulating the conformational energy of this tRNA on the ribosome so as to suppress +1 frameshifting otherwise induced by this tRNA. Six structures of E. coli ribosomal complexes carrying tRNAProL lacking m1G37 show this tRNA forms four and even five codon-anticodon base pairs as it moves into the +1 frame, allowing direct visualization of the long-standing hypothesis that a four base pair codon-anticodon can form during +1 frameshifting.

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Protein

Chemical

Disease

Primary Citation of related structures
8URM
8UTJ