› 6lk8

Electron Microscopy
5.5Å resolution

Structure of Xenopus laevis Cytoplasmic Ring subunit.

Released:
DOI: 10.2210/pdb6lk8/pdb
PDB entry 6lk8 coloured by chain, front view.
PDB entry 6lk8 coloured by chain, side view.
PDB entry 6lk8 coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex by cryo-electron microscopy single particle analysis.
Huang G, Zhang Y, Zhu X, Zeng C, Wang Q, Zhou Q, Tao Q, Liu M, Lei J, Yan C, Shi Y
OpenAccess logo Cell Res 30 520-531 (2020)
PMID: 32376910
Related structures: EMD-0909

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 32-mer (preferred)
PDBe Complex ID:
PDB-CPX-103607 (preferred)
Entry contents:
18 distinct polypeptide molecules
Macromolecules (18 distinct):
Nucleoporin 205 Chains: A, a
Molecule details ›
Chains: A, a
Length: 2011 amino acids
Theoretical weight: 227.85 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: Q642R6 (Residues: 1-2011; Coverage: 100%)
Gene names: MGC83295, nup205, nup205.L, nup205.S, xnup205
Sequence domains: Nuclear pore complex scaffold, nucleoporins 186/192/205
Nuclear pore complex protein Nup85 Chains: B, b
Molecule details ›
Chains: B, b
Length: 653 amino acids
Theoretical weight: 75.16 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: Q68FJ0 (Residues: 1-653; Coverage: 100%)
Gene name: nup85
Sequence domains: Nup85 Nucleoporin
Nucleoporin Nup43 Chains: C, c
Molecule details ›
Chains: C, c
Length: 375 amino acids
Theoretical weight: 41.74 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: Q05AW3 (Residues: 1-375; Coverage: 100%)
Gene names: MGC154553, nup43, nup43.S
Sequence domains: WD domain, G-beta repeat
Nucleoporin SEH1-A Chains: D, d
Molecule details ›
Chains: D, d
Length: 322 amino acids
Theoretical weight: 36.04 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: Q4FZW5 (Residues: 1-322; Coverage: 89%)
Gene name: seh1l-a
Sequence domains: WD domain, G-beta repeat
outer Nup160 Chains: E, e
Molecule details ›
Chains: E, e
Length: 1435 amino acids
Theoretical weight: 162.66 KDa
Source organism: Xenopus laevis
Nucleoporin Nup37 Chains: F, f
Molecule details ›
Chains: F, f
Length: 326 amino acids
Theoretical weight: 36.59 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: Q66IZ6 (Residues: 1-326; Coverage: 100%)
Gene names: MGC83926, nup37, nup37.L
Sequence domains: WD domain, G-beta repeat
Nuclear pore complex protein Nup96 Chains: G, g
Molecule details ›
Chains: G, g
Length: 923 amino acids
Theoretical weight: 105.08 KDa
Source organism: Xenopus laevis
Protein SEC13 homolog Chains: H, h
Molecule details ›
Chains: H, h
Length: 320 amino acids
Theoretical weight: 35.32 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: Q7ZYJ8 (Residues: 1-320; Coverage: 100%)
Gene names: sec13, sec13.S, sec13l1
Sequence domains: WD domain, G-beta repeat
Nuclear pore complex protein Chains: I, i
Molecule details ›
Chains: I, i
Length: 916 amino acids
Theoretical weight: 105.4 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: A2RV69 (Residues: 1-916; Coverage: 100%)
Gene names: LOC100037138, nup107, nup107.S
Sequence domains: Nuclear pore protein 84 / 107
Nucleoporin Nup133/Nup155-like N-terminal domain-containing protein Chains: J, j
Molecule details ›
Chains: J, j
Length: 1140 amino acids
Theoretical weight: 127.55 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: A0A1L8H1I9 (Residues: 1-1140; Coverage: 100%)
Gene name: nup133.L
Sequence domains: Nup133 N terminal like
RANBP2-like and GRIP domain-containing protein 3 isoform X2 Chains: S, T, U, V
Molecule details ›
Chains: S, T, U, V
Length: 2905 amino acids
Theoretical weight: 322.78 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: A0A1L8HGL2 (Residues: 1-2905; Coverage: 100%)
Gene name: ranbp2.L
Sequence domains:
Nup214 complex Coiled-coil region 1, helix 1 Chain: K
Molecule details ›
Chain: K
Length: 69 amino acids
Theoretical weight: 5.89 KDa
Source organism: Xenopus laevis
Nup214 complex coiled coil region 1, helix 2 Chain: L
Molecule details ›
Chain: L
Length: 80 amino acids
Theoretical weight: 6.83 KDa
Source organism: Xenopus laevis
Nup214 complex coiled coil region 1, helix 3 Chain: M
Molecule details ›
Chain: M
Length: 73 amino acids
Theoretical weight: 6.23 KDa
Source organism: Xenopus laevis
Nup214 complex Coiled coil region 2, helix 1 Chain: N
Molecule details ›
Chain: N
Length: 31 amino acids
Theoretical weight: 2.66 KDa
Source organism: Xenopus laevis
Nup214 complex Coiled coil region 2, helix 2 Chain: O
Molecule details ›
Chain: O
Length: 35 amino acids
Theoretical weight: 3 KDa
Source organism: Xenopus laevis
Nup214 complex Coiled coil region 2, helix 3 Chain: P
Molecule details ›
Chain: P
Length: 26 amino acids
Theoretical weight: 2.23 KDa
Source organism: Xenopus laevis
bridge domain Chains: Q, R
Molecule details ›
Chains: Q, R
Length: 391 amino acids
Theoretical weight: 33.29 KDa
Source organism: Xenopus laevis

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.5Å
Relevant EMDB volumes: EMD-0909

Quick links

Citations

11 review citations

Types of nuclear localization signals and mechanisms of protein import into the nucleus.
Lu et al. (2021)
10 more

1 mention without citation

Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold.
Fontana et al. (2022)