› 9gmo

Electron Microscopy
2.59Å resolution

eIF6-bound pre-60S large ribosomal subunit incorporating mutant uL16

Released:
DOI: 10.2210/pdb9gmo/pdb
PDB entry 9gmo coloured by chain, front view.
PDB entry 9gmo coloured by chain, side view.
PDB entry 9gmo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
ZNF574 is a Quality Control Factor For Defective Ribosome Biogenesis Intermediates.
Akers J, Bothe A, Suh H, Jung C, Stolp Z, Ghosh T, Yan L, Wang Y, Grismer T, Reyes A, Hu T, Xu S, Ban N, Kostova K
bioRxiv (2024)
PMID: 38746087
Related structures: EMD-51452

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 46-mer (preferred)
PDBe Complex ID:
PDB-CPX-302705 (preferred)
Entry contents:
43 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (46 distinct):
Large ribosomal subunit protein uL2 Chain: D
Molecule details ›
Chain: D
Length: 257 amino acids
Theoretical weight: 28.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62917 (Residues: 1-257; Coverage: 100%)
Gene name: RPL8
Sequence domains:
Large ribosomal subunit protein uL3 Chain: E
Molecule details ›
Chain: E
Length: 403 amino acids
Theoretical weight: 46.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39023 (Residues: 1-403; Coverage: 100%)
Gene names: OK/SW-cl.32, RPL3
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: F
Large ribosomal subunit protein uL18 Chain: G
Large ribosomal subunit protein eL6 Chain: H
Large ribosomal subunit protein uL13 Chain: I
Large ribosomal subunit protein uL22 Chain: J
Large ribosomal subunit protein eL18 Chain: K
Large ribosomal subunit protein eL19 Chain: L
Large ribosomal subunit protein eL20 Chain: M
Large ribosomal subunit protein eL21 Chain: N
Large ribosomal subunit protein eL22 Chain: O
Large ribosomal subunit protein uL14 Chain: P
Large ribosomal subunit protein eL24 Chain: Q
Large ribosomal subunit protein uL23 Chain: R
Large ribosomal subunit protein uL24 Chain: S
Large ribosomal subunit protein eL27 Chain: T
Large ribosomal subunit protein uL15 Chain: U
Large ribosomal subunit protein eL29 Chain: V
Large ribosomal subunit protein eL30 Chain: W
Large ribosomal subunit protein eL31 Chain: X
Large ribosomal subunit protein eL32 Chain: Y
Large ribosomal subunit protein eL33 Chain: Z
Large ribosomal subunit protein eL34 Chain: a
Large ribosomal subunit protein uL29 Chain: b
Large ribosomal subunit protein eL36 Chain: c
Large ribosomal subunit protein eL37 Chain: d
Large ribosomal subunit protein eL38 Chain: e
Large ribosomal subunit protein eL39 Chain: f
Ubiquitin-ribosomal protein eL40 fusion protein Chain: g
Eukaryotic translation initiation factor 6 Chain: h
Large ribosomal subunit protein eL42 Chain: i
Large ribosomal subunit protein eL43 Chain: j
Large ribosomal subunit protein eL28 Chain: k
Large ribosomal subunit protein eL15 Chain: l
Large ribosomal subunit protein uL30 Chain: m
Large ribosomal subunit protein eL8 Chain: n
Large ribosomal subunit protein uL6 Chain: o
Large ribosomal subunit protein uL16 Chain: p
Large ribosomal subunit protein uL5 Chain: q
Large ribosomal subunit protein eL13 Chain: r
Large ribosomal subunit protein eL14 Chain: s
Cytoplasmic 60S subunit biogenesis factor ZNF622 Chain: 0
28S ribosomal RNA Chain: A
5S ribosomal RNA Chain: B
5.8S ribosomal RNA Chain: C

Ligands and Environments

6 bound ligands:
Ligand MG 227 x MG
Ligand K 155 x K
Ligand NA 2 x NA
Ligand GTP 1 x GTP
Ligand EPE 1 x EPE
Ligand ZN 5 x ZN
9 modified residues:
Ligand A2M 21 x A2M
Ligand OMG 23 x OMG
Ligand 1MA 1 x 1MA
Ligand OMC 16 x OMC
Ligand PSU 58 x PSU
Ligand OMU 8 x OMU
Ligand 5MC 2 x 5MC
Ligand 6MZ 1 x 6MZ
Ligand UR3 1 x UR3

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 2.59Å
Relevant EMDB volumes: EMD-51452

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