8JDL image
Entry Detail
PDB ID:
8JDL
EMDB ID:
Keywords:
Title:
Structure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (non-rotated state)
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2023-05-14
Release Date:
2023-12-06
Method Details:
Experimental Method:
Resolution:
2.42 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3
Chain IDs:ZA (auth: 0)
Chain Length:243
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S4, X isoform
Chain IDs:AB (auth: 1)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S5
Chain IDs:BB (auth: 2)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S6
Chain IDs:CB (auth: 3)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S7
Chain IDs:DB (auth: 4)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S8
Chain IDs:EB (auth: 5)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S9
Chain IDs:FB (auth: 6)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S10
Chain IDs:GB (auth: 7)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S11
Chain IDs:HB (auth: 8)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S13
Chain IDs:IB (auth: 9)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:A
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S14
Chain IDs:JB (auth: AA)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15
Chain IDs:KB (auth: AB)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S16
Chain IDs:LB (auth: AC)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S17
Chain IDs:MB (auth: AD)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S18
Chain IDs:NB (auth: AE)
Chain Length:152
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S19
Chain IDs:OB (auth: AF)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S20
Chain IDs:PB (auth: AG)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S21
Chain IDs:QB (auth: AH)
Chain Length:83
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15a
Chain IDs:RB (auth: AI)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S23
Chain IDs:SB (auth: AJ)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S24
Chain IDs:TB (auth: AK)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S25
Chain IDs:UB (auth: AL)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S26
Chain IDs:VB (auth: AM)
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27
Chain IDs:WB (auth: AN)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S28
Chain IDs:XB (auth: AO)
Chain Length:69
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S29
Chain IDs:YB (auth: AP)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S30
Chain IDs:ZB (auth: AQ)
Chain Length:59
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Receptor of activated protein C kinase 1
Chain IDs:AC (auth: AR)
Chain Length:317
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:tRNA (Tyr)
Chain IDs:B
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:28S ribosomal RNA
Chain IDs:C (auth: D)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:D (auth: E)
Chain Length:120
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:5.8S ribosomal RNA
Chain IDs:E (auth: F)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8
Chain IDs:F (auth: G)
Chain Length:257
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:G (auth: H)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4
Chain IDs:H (auth: I)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L5
Chain IDs:I (auth: J)
Chain Length:297
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6
Chain IDs:J (auth: K)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7
Chain IDs:K (auth: L)
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7a
Chain IDs:L (auth: M)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9
Chain IDs:M (auth: N)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L10-like
Chain IDs:N (auth: O)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L11
Chain IDs:O (auth: P)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13
Chain IDs:P (auth: Q)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14
Chain IDs:Q (auth: R)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L15
Chain IDs:R (auth: S)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13a
Chain IDs:S (auth: T)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17
Chain IDs:T (auth: U)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18
Chain IDs:U (auth: V)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19
Chain IDs:V (auth: W)
Chain Length:1869
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18a
Chain IDs:W (auth: X)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21
Chain IDs:X (auth: Y)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22
Chain IDs:Y (auth: Z)
Chain Length:293
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23
Chain IDs:Z (auth: a)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L24
Chain IDs:AA (auth: b)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23a
Chain IDs:BA (auth: c)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26
Chain IDs:CA (auth: d)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27
Chain IDs:DA (auth: e)
Chain Length:120
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27a
Chain IDs:EA (auth: f)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:FA (auth: g)
Chain Length:257
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L30
Chain IDs:GA (auth: h)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31
Chain IDs:HA (auth: i)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:IA (auth: j)
Chain Length:297
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35a
Chain IDs:JA (auth: k)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34
Chain IDs:KA (auth: l)
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35
Chain IDs:LA (auth: m)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36
Chain IDs:MA (auth: n)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37
Chain IDs:NA (auth: o)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:OA (auth: p)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L39
Chain IDs:PA (auth: q)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ubiquitin-60S ribosomal protein L40
Chain IDs:QA (auth: r)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L41
Chain IDs:RA (auth: s)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36a
Chain IDs:SA (auth: t)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37a
Chain IDs:TA (auth: u)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28
Chain IDs:UA (auth: v)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:18S ribosomal RNA
Chain IDs:VA (auth: w)
Chain Length:1869
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein SA
Chain IDs:WA (auth: x)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3a
Chain IDs:XA (auth: y)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S2
Chain IDs:YA (auth: z)
Chain Length:293
Number of Molecules:1
Biological Source:Homo sapiens
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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Primary Citation of related structures