8UZG image
Deposition Date 2023-11-15
Release Date 2025-07-09
Last Version Date 2025-08-27
Entry Detail
PDB ID:
8UZG
Keywords:
Title:
E. coli 70S ribosome with unmodified e*/E-tRNAPro(GGG) bound to slippery P-site CCC-C codon
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
Resolution:
3.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
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:tRNA ProL(GGG)
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:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:F (auth: A)
Chain Length:229
Number of Molecules:1
Biological Source:Escherichia coli
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:57
Number of Molecules:1
Biological Source:Escherichia coli
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
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:201
Number of Molecules:1
Biological Source:Escherichia coli
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:38
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:L (auth: G)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:M (auth: J)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
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:123
Number of Molecules:1
Biological Source:Escherichia coli
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:179
Number of Molecules:1
Biological Source:Escherichia coli
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:130
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:Q (auth: N)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:R (auth: O)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:S (auth: P)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:U (auth: R)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
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:110
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:W (auth: T)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:X (auth: U)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Chain IDs:Y (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:Z (auth: W)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
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:92
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:BA (auth: Y)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:CA (auth: Z)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:DA (auth: b)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:EA (auth: c)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:FA (auth: d)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:GA (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 L36
Gene (Uniprot):rpmJ
Chain IDs:HA (auth: f)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsU
Chain IDs:IA (auth: g)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:JA (auth: h)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:KA (auth: i)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:LA (auth: j)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:MA (auth: k)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:NA (auth: l)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:OA (auth: m)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:PA (auth: n)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:QA (auth: o)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:RA (auth: p)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:SA (auth: q)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:TA (auth: r)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:UA (auth: s)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:VA (auth: t)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:WA (auth: u)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:XA (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:YA (auth: w)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:ZA (auth: x)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:AB (auth: y)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli
Ligand Molecules
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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Primary Citation of related structures