› 7wb4

Electron Microscopy
5.6Å resolution

Cryo-EM structure of the NR subunit from X. laevis NPC

Released:
DOI: 10.2210/pdb7wb4/pdb
PDB entry 7wb4 coloured by chain, front view.
PDB entry 7wb4 coloured by chain, side view.
PDB entry 7wb4 coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Cryo-EM structure of the nuclear ring from Xenopus laevis nuclear pore complex.
Huang G, Zhan X, Zeng C, Zhu X, Liang K, Zhao Y, Wang P, Wang Q, Zhou Q, Tao Q, Liu M, Lei J, Yan C, Shi Y
OpenAccess logo Cell Res 32 349-358 (2022)
PMID: 35177819
Related structures: EMD-32394

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 27-mer (preferred)
PDBe Complex ID:
PDB-CPX-103609 (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 distinct):
Nucleoporin Nup133/Nup155-like N-terminal domain-containing protein Chains: J, P, j, p
Molecule details ›
Chains: J, P, j, p
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
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 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
Nucleoporin SEH1-B Chains: D, d
Molecule details ›
Chains: D, d
Length: 360 amino acids
Theoretical weight: 39.8 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: Q6GNF1 (Residues: 1-360; Coverage: 100%)
Gene name: seh1l-b
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
Nup155-prov protein Chain: K
Molecule details ›
Chain: K
Length: 1388 amino acids
Theoretical weight: 154.92 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: Q7ZWL0 (Residues: 1-1388; Coverage: 100%)
Gene names: nup155, nup155.L
Sequence domains:
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 Nup98-Nup96 Chains: G, g
Molecule details ›
Chains: G, g
Length: 923 amino acids
Theoretical weight: 105.08 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: A0A8J1MFV7 (Residues: 863-1785; Coverage: 52%)
Gene name: nup98l.S
Sequence domains: Nuclear protein 96
Nuclear pore complex protein Chains: I, M, i
Molecule details ›
Chains: I, M, i
Length: 916 amino acids
Theoretical weight: 105.4 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: A0A8J0UTW4 (Residues: 92-1007; Coverage: 91%)
Gene names: nup107, nup107.S
Sequence domains: Nuclear pore protein 84 / 107
Nuclear pore complex protein Nup93 Chains: L, O
Molecule details ›
Chains: L, O
Length: 820 amino acids
Theoretical weight: 93.57 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: Q7ZX96 (Residues: 1-820; Coverage: 100%)
Gene name: nup93
Sequence domains: Nup93/Nic96
Nucleoporin 205 Chain: A
Molecule details ›
Chain: 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
Protein ELYS Chains: N, n
Molecule details ›
Chains: N, n
Length: 2408 amino acids
Theoretical weight: 268.77 KDa
Source organism: Xenopus laevis
UniProt:
  • Canonical: Q5U249 (Residues: 1-2408; Coverage: 100%)
Gene names: ahctf1, elys
Sequence domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.6Å
Relevant EMDB volumes: EMD-32394

Quick links

Citations

3 review citations

Nuclear transport proteins: structure, function, and disease relevance.
Yang et al. (2023)
2 more

1 mention without citation

Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex.
McCafferty et al. (2022)