9T19 image
Deposition Date 2025-10-21
Release Date 2026-03-18
Last Version Date 2026-08-26
Entry Detail
PDB ID:
9T19
Keywords:
RIBOSOME
Title:
E. coli 70S ribosome from delta-RlmE strain, PTC class 0
Biological Source:
Source Organism(s):
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.41 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9T19 validation report missing
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:tRNA(Phe)
Chain IDs:A (auth: Y)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA(fMet)
Chain IDs:B (auth: Z)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:C (auth: a)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:D (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplB
Chain IDs:E (auth: c)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplC
Chain IDs:F (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60438 Pfam ID:PF00297
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplD
Chain IDs:G (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60723 Pfam ID:PF00573
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplM
Chain IDs:H (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AA10 Pfam ID:PF00572
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplO
Chain IDs:I (auth: k)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02413 Pfam ID:PF00828
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplP
Chain IDs:J (auth: l)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A7ZSK2 Pfam ID:PF00252
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplU
Chain IDs:K (auth: q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG48 Pfam ID:PF00829
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplV
Chain IDs:L (auth: r)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P61175 Pfam ID:PF00237
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmA
Chain IDs:M (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L8 Pfam ID:PF01016
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmF
Chain IDs:N (auth: z)
Chain Length:57
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
4D4 J ARG modified residue
MEQ F GLN modified residue
Ligand Molecules
K
MG
PUT
SR0
Primary Citation
23S rRNA modifications stimulate catalytic activity and prevent the formation of alternative structures.
Nucleic Acids Res. 54 ? ? (2026)
PMID: 42598854 DOI: 10.1093/nar/gkag800

Abstact

Ribosomal RNA (rRNA) modifications cluster around the peptidyl transferase centre (PTC), the catalytic centre of the ribosome, yet their collective functional roles remain unclear. Here we analyse Escherichia coli ribosomes lacking 11 or 12 modifications near the PTC. Using kinetic assays, we show these hypo-modified ribosomes catalyse peptide bond formation at rates twofold to threefold lower than wild-type and exhibit reduced thermal stability. Cryo-electron microscopy of hypo-modified ribosomes reveals multiple alternative conformations of the PTC and exit tunnel regions, disrupting native stacking and hydrogen bonding critical for positioning of transfer RNA substrates. These findings indicate that rRNA modifications stabilize the native PTC structure, preventing formation of alternative, nonfunctional conformations and thereby enhancing catalytic efficiency. Our study provides insight into how rRNA modifications fine-tune ribosome function by maintaining structural integrity essential for efficient translation.

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Disease

Primary Citation of related structures
9T19
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