9GY4 image
Deposition Date 2024-10-01
Release Date 2025-05-14
Last Version Date 2025-05-14
Entry Detail
PDB ID:
9GY4
Keywords:
RIBOSOME
Title:
60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9GY4 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:28S rRNA
Chain IDs:A (auth: 5)
Chain Length:5070
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B (auth: 7)
Chain Length:121
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:C (auth: 8)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Nascent chain
Chain IDs:CB (auth: A)
Chain Length:7
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:CDK5 regulatory subunit-associated protein 3
Gene (Uniprot):CDK5RAP3
Chain IDs:D (auth: B)
Chain Length:506
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96JB5 Pfam ID:PF05600
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DDRGK domain-containing protein 1
Gene (Uniprot):DDRGK1
Chain IDs:E (auth: C)
Chain Length:314
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96HY6 Pfam ID:PF09756
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-fold modifier 1
Gene (Uniprot):UFM1
Chain IDs:F (auth: D)
Chain Length:85
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61960 Pfam ID:PF03671
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:E3 UFM1-protein ligase 1
Gene (Uniprot):UFL1
Chain IDs:G (auth: E)
Chain Length:794
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O94874 Pfam ID:PF09743
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase listerin
Gene (Uniprot):LTN1
Chain IDs:H (auth: F)
Chain Length:1766
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O94822 Pfam ID:PF22958, PF22999, PF23009
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:I (auth: G)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:J (auth: LB)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P39023 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Gene (Uniprot):RPL4
Chain IDs:K (auth: LC)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P36578 Pfam ID:PF00573, PF14374
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:L (auth: LD)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46777 Pfam ID:PF17144, PF14204
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL6
Gene (Uniprot):RPL6
Chain IDs:M (auth: LE)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q02878 Pfam ID:PF03868, PF01159
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):RPL7
Chain IDs:N (auth: LF)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18124 Pfam ID:PF08079, PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Gene (Uniprot):RPL7A
Chain IDs:O (auth: LG)
Chain Length:266
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62424 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Gene (Uniprot):RPL9, RPL9P7, RPL9P8, RPL9P9
Chain IDs:P (auth: LH)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P32969 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL16-like
Gene (Uniprot):RPL10L
Chain IDs:Q (auth: LI)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96L21 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Gene (Uniprot):RPL11
Chain IDs:R (auth: LJ)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62913 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Gene (Uniprot):RPL13
Chain IDs:S (auth: LL)
Chain Length:51
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P26373 Pfam ID:PF01294
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Gene (Uniprot):RPL14
Chain IDs:T (auth: LM)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P50914 Pfam ID:PF01929
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15
Gene (Uniprot):RPL15
Chain IDs:U (auth: LN)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61313 Pfam ID:PF00827
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Gene (Uniprot):RPL13A
Chain IDs:V (auth: LO)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P40429 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Gene (Uniprot):RPL17
Chain IDs:W (auth: LP)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18621 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Gene (Uniprot):RPL18
Chain IDs:X (auth: LQ)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q07020 Pfam ID:PF17135
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19
Gene (Uniprot):RPL19
Chain IDs:Y (auth: LR)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P84098 Pfam ID:PF01280
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):RPL18A
Chain IDs:Z (auth: LS)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q02543 Pfam ID:PF01775
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Gene (Uniprot):RPL21
Chain IDs:AA (auth: LT)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46778 Pfam ID:PF01157
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Gene (Uniprot):RPL22
Chain IDs:BA (auth: LU)
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P35268 Pfam ID:PF01776
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Gene (Uniprot):RPL23
Chain IDs:CA (auth: LV)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62829 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24
Gene (Uniprot):RPL24
Chain IDs:DA (auth: LW)
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P83731 Pfam ID:PF01246
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23a
Gene (Uniprot):RPL23A
Chain IDs:EA (auth: LX)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62750 Pfam ID:PF03939, PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Gene (Uniprot):RPL26
Chain IDs:FA (auth: LY)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61254 Pfam ID:PF16906, PF00467
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):RPL27
Chain IDs:GA (auth: LZ)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61353 Pfam ID:PF00467, PF01777
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27a
Gene (Uniprot):RPL27A
Chain IDs:HA (auth: La)
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46776 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:IA (auth: Lb)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P47914 Pfam ID:PF01779
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:JA (auth: Lc)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62888 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Gene (Uniprot):RPL31
Chain IDs:KA (auth: Ld)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62899 Pfam ID:PF01198
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:LA (auth: Le)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62910 Pfam ID:PF01655
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35a
Gene (Uniprot):RPL35A
Chain IDs:MA (auth: Lf)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18077 Pfam ID:PF01247
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34
Gene (Uniprot):RPL34
Chain IDs:NA (auth: Lg)
Chain Length:266
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P49207 Pfam ID:PF01199
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):RPL35
Chain IDs:OA (auth: Lh)
Chain Length:123
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P42766 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36
Chain IDs:PA (auth: Li)
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3U8 Pfam ID:PF01158
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37
Gene (Uniprot):RPL37
Chain IDs:QA (auth: Lj)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61927 Pfam ID:PF01907
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:RA (auth: Lk)
Chain Length:70
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63173 Pfam ID:PF01781
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:SA (auth: Ll)
Chain Length:51
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62891 Pfam ID:PF00832
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):UBA52
Chain IDs:TA (auth: Lm)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62987 Pfam ID:PF00240, PF01020
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36a
Gene (Uniprot):RPL36A
Chain IDs:UA (auth: Lo)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P83881 Pfam ID:PF00935
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a
Gene (Uniprot):RPL37A
Chain IDs:VA (auth: Lp)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61513 Pfam ID:PF01780
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:WA (auth: Lr)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P46779 Pfam ID:PF01778
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10a
Gene (Uniprot):RPL10A
Chain IDs:XA (auth: Lz)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62906 Pfam ID:PF00687
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome quality control complex subunit NEMF
Gene (Uniprot):NEMF
Chain IDs:YA (auth: Z)
Chain Length:1076
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O60524 Pfam ID:PF05833, PF05670, PF11923
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8
Gene (Uniprot):RPL8
Chain IDs:ZA (auth: a)
Chain Length:7
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62917 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Gene (Uniprot):RPLP0
Chain IDs:AB (auth: s)
Chain Length:317
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P05388 Pfam ID:PF00466, PF17777, PF00428
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL11
Gene (Uniprot):RPL12
Chain IDs:BB (auth: t)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P30050 Pfam ID:PF03946, PF00298
Ligand Molecules
MG
ZN
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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
9GY4
Feedback Form
Name
Email
Institute
Feedback