› 7r5k

Electron Microscopy
12Å resolution

Human nuclear pore complex (constricted)

Released:
DOI: 10.2210/pdb7r5k/pdb
PDB entry 7r5k coloured by chain, front view.
PDB entry 7r5k coloured by chain, side view.
PDB entry 7r5k coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Mosalaganti S, Obarska-Kosinska A, Siggel M, Taniguchi R, Turonova B, Zimmerli CE, Buczak K, Schmidt FH, Margiotta E, Mackmull MT, Hagen WJH, Hummer G, Kosinski J, Beck M
Related structures: EMD-14322

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 808-mer (preferred)
PDBe Complex ID:
PDB-CPX-131102 (preferred)
Entry contents:
25 distinct polypeptide molecules
Macromolecules (25 distinct):
E3 SUMO-protein ligase RanBP2 Chains: 00, 01, 02, 03, 04
Molecule details ›
Chains: 00, 01, 02, 03, 04
Length: 3224 amino acids
Theoretical weight: 358.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49792 (Residues: 1-3224; Coverage: 100%)
Gene names: NUP358, RANBP2
Sequence domains:
Nuclear pore membrane glycoprotein 210 Chains: 10, 11, 12, 13, 14, 15, 16, 17
Molecule details ›
Chains: 10, 11, 12, 13, 14, 15, 16, 17
Length: 1887 amino acids
Theoretical weight: 205.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8TEM1 (Residues: 1-1887; Coverage: 100%)
Gene names: KIAA0906, NUP210, PSEC0245
Sequence domains:
Aladin Chains: 40, 41
Molecule details ›
Chains: 40, 41
Length: 546 amino acids
Theoretical weight: 59.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NRG9 (Residues: 1-546; Coverage: 100%)
Gene names: AAAS, ADRACALA, GL003
Sequence domains: WD domain, G-beta repeat
Nuclear pore complex protein Nup93 Chains: A0, A1, A2, A3, A4, A5, A6
Molecule details ›
Chains: A0, A1, A2, A3, A4, A5, A6
Length: 819 amino acids
Theoretical weight: 93.6 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8N1F7 (Residues: 1-819; Coverage: 100%)
Gene names: KIAA0095, NUP93
Sequence domains: Nup93/Nic96
Nucleoporin NUP188 Chains: B0, B1
Molecule details ›
Chains: B0, B1
Length: 1749 amino acids
Theoretical weight: 196.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q5SRE5 (Residues: 1-1749; Coverage: 100%)
Gene names: KIAA0169, NUP188
Sequence domains:
Nuclear pore complex protein Nup205 Chains: C0, C1, C2, C3, C4
Molecule details ›
Chains: C0, C1, C2, C3, C4
Length: 2012 amino acids
Theoretical weight: 228.17 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q92621 (Residues: 1-2012; Coverage: 100%)
Gene names: C7orf14, KIAA0225, NUP205
Sequence domains: Nuclear pore complex scaffold, nucleoporins 186/192/205
Nuclear pore complex protein Nup155 Chains: D0, D1, D2, D3, D4, D5
Molecule details ›
Chains: D0, D1, D2, D3, D4, D5
Length: 1391 amino acids
Theoretical weight: 155.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75694 (Residues: 1-1391; Coverage: 100%)
Gene names: KIAA0791, NUP155
Sequence domains:
Nucleoporin NDC1 Chains: E0, E1
Molecule details ›
Chains: E0, E1
Length: 674 amino acids
Theoretical weight: 76.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BTX1 (Residues: 1-674; Coverage: 100%)
Gene names: NDC1, TMEM48
Sequence domains: Nucleoporin protein Ndc1-Nup
Nucleoporin NUP35 Chains: F0, F1, F2, F3
Molecule details ›
Chains: F0, F1, F2, F3
Length: 326 amino acids
Theoretical weight: 34.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8NFH5 (Residues: 1-326; Coverage: 100%)
Gene names: MP44, NUP35, NUP53
Sequence domains: Nup53/35/40-type RNA recognition motif
Nucleoporin p54 Chains: H0, H1, H2, H3
Molecule details ›
Chains: H0, H1, H2, H3
Length: 507 amino acids
Theoretical weight: 55.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q7Z3B4 (Residues: 1-507; Coverage: 100%)
Gene name: NUP54
Sequence domains:
Nucleoporin p58/p45 Chains: I0, I1, I2, I3
Molecule details ›
Chains: I0, I1, I2, I3
Length: 599 amino acids
Theoretical weight: 60.94 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BVL2 (Residues: 1-599; Coverage: 100%)
Gene names: KIAA0410, NUP58, NUPL1
Sequence domains: Nucleoporin FG repeated region
Nuclear pore glycoprotein p62 Chains: J0, J1, J2, J3, J4
Molecule details ›
Chains: J0, J1, J2, J3, J4
Length: 522 amino acids
Theoretical weight: 53.29 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P37198 (Residues: 1-522; Coverage: 100%)
Gene name: NUP62
Sequence domains: Nsp1-like C-terminal region
Nuclear pore complex protein Nup133 Chains: K0, K1, K2, K3
Molecule details ›
Chains: K0, K1, K2, K3
Length: 1156 amino acids
Theoretical weight: 129.11 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8WUM0 (Residues: 1-1156; Coverage: 100%)
Gene name: NUP133
Sequence domains: Non-repetitive/WGA-negative nucleoporin C-terminal
Nuclear pore complex protein Nup107 Chains: L0, L1, L2, L3
Molecule details ›
Chains: L0, L1, L2, L3
Length: 925 amino acids
Theoretical weight: 106.5 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P57740 (Residues: 1-925; Coverage: 100%)
Gene name: NUP107
Sequence domains: Nuclear pore protein 84 / 107
Nuclear pore complex protein Nup96 Chains: M0, M1, M2, M3
Molecule details ›
Chains: M0, M1, M2, M3
Length: 937 amino acids
Theoretical weight: 106.04 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P52948 (Residues: 881-1817; Coverage: 52%)
Gene names: ADAR2, NUP98
Sequence domains: Nuclear protein 96
Protein SEC13 homolog Chains: N0, N1, N2, N3
Molecule details ›
Chains: N0, N1, N2, N3
Length: 322 amino acids
Theoretical weight: 35.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P55735 (Residues: 1-322; Coverage: 100%)
Gene names: D3S1231E, SEC13, SEC13A, SEC13L1, SEC13R
Sequence domains: WD domain, G-beta repeat
Nucleoporin SEH1 Chains: O0, O1, O2, O3
Molecule details ›
Chains: O0, O1, O2, O3
Length: 360 amino acids
Theoretical weight: 39.7 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96EE3 (Residues: 1-360; Coverage: 100%)
Gene names: SEC13L, SEH1, SEH1L
Sequence domains: WD domain, G-beta repeat
Nuclear pore complex protein Nup85 Chains: P0, P1, P2, P3
Molecule details ›
Chains: P0, P1, P2, P3
Length: 656 amino acids
Theoretical weight: 75.11 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BW27 (Residues: 1-656; Coverage: 100%)
Gene names: NUP75, NUP85, PCNT1
Sequence domains: Nup85 Nucleoporin
Nucleoporin Nup43 Chains: Q0, Q1, Q2, Q3
Molecule details ›
Chains: Q0, Q1, Q2, Q3
Length: 380 amino acids
Theoretical weight: 42.2 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8NFH3 (Residues: 1-380; Coverage: 100%)
Gene name: NUP43
Sequence domains: WD domain, G-beta repeat
Nuclear pore complex protein Nup160 Chains: R0, R1, R2, R3
Molecule details ›
Chains: R0, R1, R2, R3
Length: 1436 amino acids
Theoretical weight: 162.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q12769 (Residues: 1-1436; Coverage: 100%)
Gene names: KIAA0197, NUP120, NUP160
Sequence domains: Nucleoporin Nup120/160
Nucleoporin Nup37 Chains: S0, S1, S2, S3
Molecule details ›
Chains: S0, S1, S2, S3
Length: 326 amino acids
Theoretical weight: 36.75 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8NFH4 (Residues: 1-326; Coverage: 100%)
Gene name: NUP37
Sequence domains: WD domain, G-beta repeat
Protein ELYS Chains: T0, T1
Molecule details ›
Chains: T0, T1
Length: 2266 amino acids
Theoretical weight: 252.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8WYP5 (Residues: 1-2266; Coverage: 100%)
Gene names: AHCTF1, ELYS, MSTP108, TMBS62
Sequence domains:
Nuclear pore complex protein Nup98 Chains: U0, U1, U2, U3, U4, U5, U6
Molecule details ›
Chains: U0, U1, U2, U3, U4, U5, U6
Length: 880 amino acids
Theoretical weight: 91.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P52948 (Residues: 1-880; Coverage: 48%)
Gene names: ADAR2, NUP98
Sequence domains:
Nuclear pore complex protein Nup214 Chain: V0
Molecule details ›
Chain: V0
Length: 2090 amino acids
Theoretical weight: 213.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P35658 (Residues: 1-2090; Coverage: 100%)
Gene names: CAIN, CAN, KIAA0023, NUP214
Sequence domains: Nucleoporin Nup214 phenylalanine-glycine (FG) domain
Nuclear pore complex protein Nup88 Chain: W0
Molecule details ›
Chain: W0
Length: 741 amino acids
Theoretical weight: 83.64 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99567 (Residues: 1-741; Coverage: 100%)
Gene name: NUP88
Sequence domains: Nuclear pore component

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 12Å
Relevant EMDB volumes: EMD-14322

Quick links

Citations

11 review citations

Bringing Structure to Cell Biology with Cryo-Electron Tomography.
Young et al. (2023)
10 more

4 mentions without citation

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future.
Burley et al. (2022)
3 more