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› 8ink

Electron Microscopy
3.2Å resolution

human nuclear pre-60S ribosomal particle - State D

Released:
DOI: 10.2210/pdb8ink/pdb
PDB entry 8ink coloured by chain, front view.
PDB entry 8ink coloured by chain, side view.
PDB entry 8ink coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
Zhang Y, Liang X, Luo S, Chen Y, Li Y, Ma C, Li N, Gao N
Cell Res (2023)
PMID: 37491604
Related structures: EMD-35599

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 53-mer (preferred)
PDBe Complex ID:
PDB-CPX-301009 (preferred)
Entry contents:
50 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (53 distinct):
Protein SDA1 homolog Chain: N
Molecule details ›
Chain: N
Length: 687 amino acids
Theoretical weight: 80.01 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NVU7 (Residues: 1-687; Coverage: 100%)
Gene names: NUC130, SDAD1
Sequence domains:
Eukaryotic translation initiation factor 6 Chain: 6
Molecule details ›
Chain: 6
Length: 245 amino acids
Theoretical weight: 26.62 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P56537 (Residues: 1-245; Coverage: 100%)
Gene names: EIF3A, EIF6, ITGB4BP, OK/SW-cl.27
Sequence domains: eIF-6 family
Probable ribosome biogenesis protein RLP24 Chain: 7
Zinc finger protein 593 Chain: 9
Large ribosomal subunit protein eL29 Chain: A
Large ribosomal subunit protein uL3 Chain: B
Large ribosomal subunit protein uL4 Chain: D
Large ribosomal subunit protein eL30 Chain: E
Large ribosomal subunit protein eL34 Chain: F
Large ribosomal subunit protein eL8 Chain: G
Large ribosomal subunit protein uL29 Chain: H
Large ribosomal subunit protein uL6 Chain: I
Ribosome biogenesis protein NSA2 homolog Chain: J
Large ribosomal subunit protein eL36 Chain: K
Large ribosomal subunit protein uL15 Chain: L
Large ribosomal subunit protein eL37 Chain: M
Large ribosomal subunit protein eL38 Chain: O
Large ribosomal subunit protein eL39 Chain: P
Large ribosomal subunit protein eL13 Chain: Q
Large ribosomal subunit protein eL14 Chain: S
Large ribosomal subunit protein eL15 Chain: U
Large ribosomal subunit protein uL13 Chain: V
Large ribosomal subunit protein eL43 Chain: X
Large ribosomal subunit protein eL18 Chain: Z
Large ribosomal subunit protein eL19 Chain: a
Large ribosomal subunit protein eL20 Chain: b
Large ribosomal subunit protein uL14 Chain: e
Large ribosomal subunit protein uL23 Chain: g
Large ribosomal subunit protein uL24 Chain: h
Large ribosomal subunit protein eL27 Chain: i
Large ribosomal subunit protein eL28 Chain: l
Large ribosomal subunit protein uL2 Chain: m
Large ribosomal subunit protein eL33 Chain: n
Large ribosomal subunit protein eL6 Chain: o
Large ribosomal subunit protein uL30 Chain: p
Coiled-coil domain-containing protein 86 Chain: r
Guanine nucleotide-binding protein-like 3 Chain: u
Nucleolar GTP-binding protein 2 Chain: w
Large ribosomal subunit protein uL11 Chain: y
Protein LLP homolog Chain: z
Large ribosomal subunit protein uL5 Chain: C
Large ribosomal subunit protein uL18 Chain: R
Notchless protein homolog 1 Chain: W
Large ribosomal subunit protein eL21 Chain: T
GTP-binding protein 4 Chain: 4
Large ribosomal subunit protein uL22 Chain: Y
Large ribosomal subunit protein eL32 Chain: k
Large ribosomal subunit protein eL31 Chain: j
Large ribosomal subunit protein eL22 Chain: d
mRNA turnover protein 4 homolog Chain: v
5.8S ribosomal RNA Chain: 8
5S ribosomal RNA Chain: 3
28S ribosomal RNA Chain: 2

Ligands and Environments

2 bound ligands:
Ligand GTP 1 x GTP
Ligand MG 1 x MG
23 modified residues:
Ligand OMU 2 x OMU
Ligand B9B 3 x B9B
Ligand OMG 14 x OMG
Ligand A2M 13 x A2M
Ligand 2MG 4 x 2MG
Ligand 1MA 1 x 1MA
Ligand P4U 1 x P4U
Ligand B8Q 1 x B8Q
Ligand 7MG 3 x 7MG
Ligand I4U 1 x I4U
Ligand P7G 2 x P7G
Ligand E7G 1 x E7G
Ligand OMC 9 x OMC
Ligand B8W 5 x B8W
Ligand B9H 1 x B9H
Ligand B8K 2 x B8K
Ligand BGH 1 x BGH
Ligand 5MU 1 x 5MU
Ligand 6MZ 1 x 6MZ
Ligand 5MC 1 x 5MC
Ligand B8T 2 x B8T
Ligand UR3 2 x UR3
Ligand M7A 1 x M7A

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.2Å
Relevant EMDB volumes: EMD-35599

Quick links

Citations

1 citations in other articles

Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Thoms et al. (2023)