9GY4 image
Entry Detail
PDB ID:
9GY4
EMDB ID:
Keywords:
Title:
60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map)
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2024-10-01
Release Date:
2025-05-14
Method Details:
Experimental Method:
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:28S rRNA
Chain IDs:A (auth: 5)
Chain Length:5070
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:B (auth: 7)
Chain Length:121
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:5.8S rRNA
Chain IDs:C (auth: 8)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Nascent chain
Chain IDs:CB (auth: A)
Chain Length:7
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:CDK5 regulatory subunit-associated protein 3
Chain IDs:D (auth: B)
Chain Length:506
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:DDRGK domain-containing protein 1
Chain IDs:E (auth: C)
Chain Length:314
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ubiquitin-fold modifier 1
Chain IDs:F (auth: D)
Chain Length:85
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:E3 UFM1-protein ligase 1
Chain IDs:G (auth: E)
Chain Length:794
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:E3 ubiquitin-protein ligase listerin
Chain IDs:H (auth: F)
Chain Length:1766
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:tRNA
Chain IDs:I (auth: G)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:J (auth: LB)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4
Chain IDs:K (auth: LC)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L5
Chain IDs:L (auth: LD)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein eL6
Chain IDs:M (auth: LE)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL30
Chain IDs:N (auth: LF)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7a
Chain IDs:O (auth: LG)
Chain Length:266
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9
Chain IDs:P (auth: LH)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL16-like
Chain IDs:Q (auth: LI)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L11
Chain IDs:R (auth: LJ)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13
Chain IDs:S (auth: LL)
Chain Length:51
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14
Chain IDs:T (auth: LM)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L15
Chain IDs:U (auth: LN)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13a
Chain IDs:V (auth: LO)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17
Chain IDs:W (auth: LP)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18
Chain IDs:X (auth: LQ)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19
Chain IDs:Y (auth: LR)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18a
Chain IDs:Z (auth: LS)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21
Chain IDs:AA (auth: LT)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22
Chain IDs:BA (auth: LU)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23
Chain IDs:CA (auth: LV)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L24
Chain IDs:DA (auth: LW)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23a
Chain IDs:EA (auth: LX)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26
Chain IDs:FA (auth: LY)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27
Chain IDs:GA (auth: LZ)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27a
Chain IDs:HA (auth: La)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:IA (auth: Lb)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L30
Chain IDs:JA (auth: Lc)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31
Chain IDs:KA (auth: Ld)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:LA (auth: Le)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35a
Chain IDs:MA (auth: Lf)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34
Chain IDs:NA (auth: Lg)
Chain Length:266
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35
Chain IDs:OA (auth: Lh)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36
Chain IDs:PA (auth: Li)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37
Chain IDs:QA (auth: Lj)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:RA (auth: Lk)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L39
Chain IDs:SA (auth: Ll)
Chain Length:51
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ubiquitin-60S ribosomal protein L40
Chain IDs:TA (auth: Lm)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36a
Chain IDs:UA (auth: Lo)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37a
Chain IDs:VA (auth: Lp)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28
Chain IDs:WA (auth: Lr)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L10a
Chain IDs:XA (auth: Lz)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ribosome quality control complex subunit NEMF
Chain IDs:YA (auth: Z)
Chain Length:1076
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8
Chain IDs:ZA (auth: a)
Chain Length:7
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S acidic ribosomal protein P0
Chain IDs:AB (auth: s)
Chain Length:317
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL11
Chain IDs:BB (auth: t)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
UFMylation orchestrates spatiotemporal coordination of RQC at the ER.
Sci Adv 11 eadv0435 eadv0435 (2025)
PMID: 40315331 DOI: 10.1126/sciadv.adv0435

Abstact

Degradation of arrest peptides from endoplasmic reticulum (ER) translocon-bound 60S ribosomal subunits via the ribosome-associated quality control (ER-RQC) pathway requires covalent modification of RPL26/uL24 on 60S ribosomal subunits with UFM1. However, the underlying mechanism that coordinates the UFMylation and RQC pathways remains elusive. Structural analysis of ER-RQC intermediates revealed concomitant binding and direct interaction of the UFMylation and RQC machineries on the 60S. In the presence of an arrested peptidyl-transfer RNA, the RQC factor NEMF and the UFM1 E3 ligase (E3UFM1) form a direct interaction via the UFL1 subunit of E3UFM1, and UFL1 adopts a conformation distinct from that previously observed for posttermination 60S. While this concomitant binding occurs on translocon-bound 60S, LTN1 recruitment and arrest peptide degradation require UFMylation-dependent 60S dissociation from the translocon. These data reveal a mechanism by which the UFMylation cycle orchestrates ER-RQC.

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Primary Citation of related structures