9OFV image
Deposition Date 2025-04-30
Release Date 2025-06-11
Last Version Date 2025-07-16
Entry Detail
PDB ID:
9OFV
Keywords:
STRUCTURAL PROTEIN
Title:
Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 4932)
Host Organism:
Saccharomyces cerevisiae
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.16 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9OFV validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Gene (Uniprot):RPP0
Chain IDs:EB (auth: 0)
Chain Length:312
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05317 Pfam ID:PF17777, PF00466, PF00428
Polymer Type:polypeptide(L)
Molecule:CAT-tailed nascent peptide
Chain IDs:FB (auth: 1)
Chain Length:17
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Polyubiquitin-C
Gene (Uniprot):UBC
Chain IDs:JB (auth: 2)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CG64 Pfam ID:PF00240
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:K (auth: 3)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05740 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:L (auth: 4)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX49 Pfam ID:PF17135
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:M (auth: 5)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX82 Pfam ID:PF01280
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20-A
Gene (Uniprot):RPL20A
Chain IDs:N (auth: 6)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX23 Pfam ID:PF01775
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:O (auth: 7)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02753 Pfam ID:PF01157
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:P (auth: 8)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05749 Pfam ID:PF01776
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL24A
Gene (Uniprot):RPL24A
Chain IDs:R (auth: 9)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04449 Pfam ID:PF01246
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cell division control protein 48
Gene (Uniprot):CDC48
Chain IDs:A, B, C, D, E, F
Chain Length:1038
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25694 Pfam ID:PF02933, PF00004, PF17862, PF02359
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nuclear protein localization protein 4
Gene (Uniprot):NPL4
Chain IDs:J (auth: G)
Chain Length:580
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P33755 Pfam ID:PF05020, PF05021
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:Q (auth: I)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX41 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Gene (Uniprot):UBI4
Chain IDs:G (auth: K), H, I (auth: J)
Chain Length:76
Number of Molecules:3
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CG63 Pfam ID:PF00240
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:S (auth: L)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:T (auth: M)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H6 Pfam ID:PF01777
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:U (auth: N)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P02406 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL29
Gene (Uniprot):RPL29
Chain IDs:V (auth: O)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05747 Pfam ID:PF01779
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:W (auth: P)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14120 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:X (auth: Q)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H8 Pfam ID:PF01198
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL32
Gene (Uniprot):RPL32
Chain IDs:Y (auth: R)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38061 Pfam ID:PF01655
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:Z (auth: S)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05744 Pfam ID:PF01247
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:AA (auth: T)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P87262 Pfam ID:PF01199
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:BA (auth: U)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX84 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:CA (auth: V)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05745 Pfam ID:PF01158
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:DA (auth: W)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49166 Pfam ID:PF01907
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL38
Gene (Uniprot):RPL38
Chain IDs:HB (auth: X)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49167 Pfam ID:PF01781
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:EA (auth: Y)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04650 Pfam ID:PF00832
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):RPL40A
Chain IDs:FA (auth: Z)
Chain Length:165
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CH08 Pfam ID:PF00240, PF01020
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome quality control complex subunit 2
Gene (Uniprot):RQC2
Chain IDs:YA (auth: a)
Chain Length:1038
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12532 Pfam ID:PF05833, PF05670, PF11923
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:KB (auth: a0)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26784 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Gene (Uniprot):RPL42A
Chain IDs:GA (auth: b)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX27 Pfam ID:PF00935
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:LB (auth: b0)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04456 Pfam ID:PF03939, PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:HA (auth: c)
Chain Length:835
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX25 Pfam ID:PF01780
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41-A
Gene (Uniprot):RPL41A
Chain IDs:IA (auth: d)
Chain Length:25
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX86 Pfam ID:PF05162
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase listerin
Gene (Uniprot):RKR1
Chain IDs:ZA (auth: e)
Chain Length:1562
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q04781 Pfam ID:PF22958, PF13639, PF22999, PF23009
Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:JA (auth: f)
Chain Length:835
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):TIF6
Chain IDs:AB (auth: g)
Chain Length:580
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12522 Pfam ID:PF01912
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:KA (auth: h)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:LA (auth: i)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:MA (auth: j)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX45 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Gene (Uniprot):RPL3
Chain IDs:NA (auth: k)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14126 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4A
Gene (Uniprot):RPL4A
Chain IDs:OA (auth: l)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P10664 Pfam ID:PF00573, PF14374
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):RPL5
Chain IDs:PA (auth: m)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26321 Pfam ID:PF17144, PF14204
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL6B
Gene (Uniprot):RPL6B
Chain IDs:QA (auth: n)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05739 Pfam ID:PF01159
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:RA (auth: o)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05737 Pfam ID:PF08079, PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:SA (auth: p)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P17076 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:TA (auth: q)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05738 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16
Gene (Uniprot):RPL10
Chain IDs:UA (auth: r)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41805 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5A
Gene (Uniprot):RPL11A
Chain IDs:VA (auth: s)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0W9 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:WA (auth: t)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12690 Pfam ID:PF01294
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:XA (auth: u)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36105 Pfam ID:PF00467, PF01929
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome quality control complex subunit 1
Gene (Uniprot):RQC1
Chain IDs:IB (auth: v)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q05468 Pfam ID:PF04910
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL1A
Gene (Uniprot):RPL1A
Chain IDs:GB (auth: w)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX43 Pfam ID:PF00687
Polymer Type:polyribonucleotide
Molecule:Ala tRNA
Chain IDs:BB (auth: x), CB (auth: y)
Chain Length:76
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL11A
Gene (Uniprot):RPL12A
Chain IDs:DB (auth: z)
Chain Length:165
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX53 Pfam ID:PF00298, PF03946
Ligand Molecules
ADP
ATP
MG
SPD
ZN
Primary Citation
Mechanism of nascent chain removal by the ribosome-associated quality control complex.
Nat Commun 16 5792 5792 (2025)
PMID: 40595698 DOI: 10.1038/s41467-025-61235-w

Abstact

Errors during translation can cause ribosome stalling, leaving incomplete nascent chains attached to large ribosomal subunits. Cells rely on the Ribosome-associated Quality Control (RQC) complex to recognize, process, and remove these aberrant proteins to maintain proteostasis. Despite its importance, the mechanisms by which the RQC orchestrates nascent chain processing and extraction have remained unclear. Here, we present a cryo-EM structure of the RQC complex from budding yeast, revealing how its core components function in nascent chain removal. We show that the Cdc48 ATPase and its Ufd1-Npl4 adaptor are recruited by the Ltn1 E3 ubiquitin ligase to extract ubiquitylated peptides from the 60S ribosome. Additionally, we find that Rqc1 bridges the 60S subunit with ubiquitin and Ltn1, facilitating formation of K48-linked polyubiquitin chains. These findings provide a structural and mechanistic framework for understanding how the RQC complex collaborates to clear stalled translation products, advancing insight into cellular protein quality control.

Legend

Protein

Chemical

Disease

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