7Y7E image
Entry Detail
PDB ID:
7Y7E
EMDB ID:
Keywords:
Title:
Structure of the Bacterial Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU)
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2022-06-22
Release Date:
2023-10-25
Method Details:
Experimental Method:
Resolution:
2.41 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:VA (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:WA (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:XA (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:YA (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31
Chain IDs:ZA (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:A
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:B
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:C
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:D
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:E
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6, fully modified isoform
Chain IDs:F
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:G
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:H
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:I
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:J
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:K
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:L
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:M
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14
Chain IDs:N
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:O
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:P
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:Q
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:R
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:S
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:T
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S21
Chain IDs:U
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:A-site tRNA-Asp
Chain IDs:CB (auth: V)
Chain Length:85
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:AB (auth: X)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:P-site tRNA-fMet
Chain IDs:BB (auth: Z)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:23S rRNA
Chain IDs:V (auth: a)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:W (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:X (auth: c)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:Y (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:Z (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:AA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:BA (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:CA (auth: h)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:DA (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:EA (auth: j)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:FA (auth: k)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:GA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:HA (auth: m)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:IA (auth: n)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:JA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:KA (auth: p)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:LA (auth: q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:MA (auth: r)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:NA (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:OA (auth: t)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:PA (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:QA (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:RA (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:SA (auth: x)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:TA (auth: y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:UA (auth: z)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG A G modified residue
4D4 GA ARG modified residue
4OC A C modified residue
4SU BB U modified residue
5MC A C modified residue
5MU BB U modified residue
D2T L ASP modified residue
G7M A G modified residue
H2U BB U modified residue
MA6 A A modified residue
MEQ Y GLN modified residue
OMC BB C modified residue
PSU A U modified residue
UR3 A U modified residue
Primary Citation
Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.
Cell 186 5517 ? (2023)
PMID: 37992713 DOI: 10.1016/j.cell.2023.10.026

Abstact

Transfer RNA (tRNA) modifications are critical for protein synthesis. Queuosine (Q), a 7-deaza-guanosine derivative, is present in tRNA anticodons. In vertebrate tRNAs for Tyr and Asp, Q is further glycosylated with galactose and mannose to generate galQ and manQ, respectively. However, biogenesis and physiological relevance of Q-glycosylation remain poorly understood. Here, we biochemically identified two RNA glycosylases, QTGAL and QTMAN, and successfully reconstituted Q-glycosylation of tRNAs using nucleotide diphosphate sugars. Ribosome profiling of knockout cells revealed that Q-glycosylation slowed down elongation at cognate codons, UAC and GAC (GAU), respectively. We also found that galactosylation of Q suppresses stop codon readthrough. Moreover, protein aggregates increased in cells lacking Q-glycosylation, indicating that Q-glycosylation contributes to proteostasis. Cryo-EM of human ribosome-tRNA complex revealed the molecular basis of codon recognition regulated by Q-glycosylations. Furthermore, zebrafish qtgal and qtman knockout lines displayed shortened body length, implying that Q-glycosylation is required for post-embryonic growth in vertebrates.

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