› 6xir

Electron Microscopy
3.2Å resolution

Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress

Released:
DOI: 10.2210/pdb6xir/pdb
PDB entry 6xir coloured by chain, front view.
PDB entry 6xir coloured by chain, side view.
PDB entry 6xir coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.
Zhou Y, Kastritis PL, Dougherty SE, Bouvette J, Hsu AL, Burbaum L, Mosalaganti S, Pfeffer S, Hagen WJH, Förster F, Borgnia MJ, Vogel C, Beck M, Bartesaghi A, Silva GM
Proc Natl Acad Sci U S A 117 22157-22166 (2020)
PMID: 32855298
Related structures: EMD-22198

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 76-mer (preferred)
PDBe Complex ID:
PDB-CPX-282615 (preferred)
Entry contents:
70 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (75 distinct):
Large ribosomal subunit protein uL2A Chain: A
Molecule details ›
Chain: A
Length: 254 amino acids
Theoretical weight: 27.46 KDa
Source organism: Saccharomyces cerevisiae
RPL3 isoform 1 Chain: B
Molecule details ›
Chain: B
Length: 387 amino acids
Theoretical weight: 43.85 KDa
Source organism: Saccharomyces cerevisiae
RPL4A isoform 1 Chain: C
RPL5 isoform 1 Chain: D
Large ribosomal subunit protein eL6A Chain: E
Large ribosomal subunit protein uL30A Chain: F
RPL8A isoform 1 Chain: G
RPL9A isoform 1 Chain: H
RPL10 isoform 1 Chain: I
RPL11B isoform 1 Chain: J
Large ribosomal subunit protein eL13A Chain: L
Large ribosomal subunit protein eL14A Chain: M
Large ribosomal subunit protein eL15A Chain: N
Large ribosomal subunit protein uL13A Chain: O
Large ribosomal subunit protein uL22A Chain: P
Large ribosomal subunit protein eL18A Chain: Q
Large ribosomal subunit protein eL19A Chain: R
Large ribosomal subunit protein eL20A Chain: S
Large ribosomal subunit protein eL21A Chain: T
Large ribosomal subunit protein eL22A Chain: U
Large ribosomal subunit protein uL14A Chain: V
RPL24A isoform 1 Chain: W
Large ribosomal subunit protein uL23 Chain: X
Large ribosomal subunit protein uL24A Chain: Y
Large ribosomal subunit protein eL27A Chain: Z
Small ribosomal subunit protein eS10A Chain: AA
Small ribosomal subunit protein uS17A Chain: AB
Large ribosomal subunit protein uL15 Chain: a
RPL29 isoform 1 Chain: b
Large ribosomal subunit protein eL30 Chain: c
Large ribosomal subunit protein eL31A Chain: d
RPL32 isoform 1 Chain: e
Large ribosomal subunit protein eL33A Chain: f
Large ribosomal subunit protein eL34A Chain: g
Large ribosomal subunit protein uL29A Chain: h
Large ribosomal subunit protein eL36A Chain: i
Large ribosomal subunit protein eL37A Chain: j
RPL38 isoform 1 Chain: k
Large ribosomal subunit protein eL39 Chain: l
RPL41A isoform 1 Chain: n
Large ribosomal subunit protein eL42A Chain: o
Large ribosomal subunit protein eL43A Chain: p
Small ribosomal subunit protein uS2A Chain: q
RPS1A isoform 1 Chain: r
RPS2 isoform 1 Chain: s
RPS3 isoform 1 Chain: t
Small ribosomal subunit protein eS4A Chain: u
Rps5p Chain: v
Small ribosomal subunit protein eS6A Chain: w
Small ribosomal subunit protein eS7A Chain: x
RPS8A isoform 1 Chain: y
Small ribosomal subunit protein uS4A Chain: z
Small ribosomal subunit protein uS15 Chain: AD
Small ribosomal subunit protein uS11B Chain: AE
RPS15 isoform 1 Chain: AF
Small ribosomal subunit protein uS9A Chain: AG
Small ribosomal subunit protein eS17B Chain: AH
Small ribosomal subunit protein uS13A Chain: AI
Small ribosomal subunit protein eS19A Chain: AJ
RPS20 isoform 1 Chain: AK
Small ribosomal subunit protein eS21A Chain: AL
RPS22A isoform 1 Chain: AM
Small ribosomal subunit protein uS12A Chain: AN
Small ribosomal subunit protein eS24A Chain: AO
RPS25A isoform 1 Chain: AP
RPS26B isoform 1 Chain: AQ
Small ribosomal subunit protein eS27A Chain: AR
RPS28A isoform 1 Chain: AS
RPS29A isoform 1 Chain: AT
Small ribosomal subunit protein RACK1 Chain: AV
35S ribosomal RNA Chain: 1
5S ribosomal RNA Chain: 3
5.8S ribosomal RNA Chain: 4
18S Ribosomal RNA Chain: 2
Transfer RNA Chains: AX, AZ

Ligands and Environments

1 bound ligand:
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-22198

Quick links

Citations

4 review citations

Deubiquitinating enzymes (DUBs): Regulation, homeostasis, and oxidative stress response.
Snyder et al. (2021)
3 more

1 mention without citation

Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome.
Hassan et al. (2023)