9HCJ image
Entry Detail
PDB ID:
9HCJ
EMDB ID:
Keywords:
Title:
D. discoideum nuclear pore complex
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2024-11-10
Release Date:
2024-12-25
Method Details:
Experimental Method:
Resolution:
30.00 Å
Aggregation State:
CELL
Reconstruction Method:
SUBTOMOGRAM AVERAGING
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:RanBP2-type zinc finger
Chain IDs:A (auth: 00), B (auth: 01)
Chain Length:3566
Number of Molecules:2
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nucleoporin 210
Chain IDs:C (auth: 10), D (auth: 11), E (auth: 12), F (auth: 13), G (auth: 14), H (auth: 15), I (auth: 16), J (auth: 17)
Chain Length:1916
Number of Molecules:8
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:WD40 repeat-containing protein
Chain IDs:K (auth: 40), L (auth: 41)
Chain Length:471
Number of Molecules:2
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nuclear pore protein
Chain IDs:M (auth: A0), N (auth: A1), O (auth: A2), P (auth: A3), Q (auth: A4), R (auth: A5)
Chain Length:979
Number of Molecules:6
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nup188
Chain IDs:S (auth: B0), T (auth: B1)
Chain Length:2174
Number of Molecules:2
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nup205
Chain IDs:U (auth: C0), V (auth: C1), W (auth: C2), X (auth: C3)
Chain Length:1916
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nucleoporin 155
Chain IDs:Y (auth: D0), Z (auth: D1), AA (auth: D2), BA (auth: D3)
Chain Length:1575
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:NDC1
Chain IDs:CA (auth: E0), DA (auth: E1)
Chain Length:667
Number of Molecules:2
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nup35
Chain IDs:EA (auth: F0), FA (auth: F1), GA (auth: F2), HA (auth: F3)
Chain Length:95
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nuclear pore complex protein nup54
Chain IDs:IA (auth: H0), JA (auth: H1), KA (auth: H2), LA (auth: H3)
Chain Length:440
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nup58
Chain IDs:MA (auth: I0), NA (auth: I1), OA (auth: I2), PA (auth: I3)
Chain Length:581
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nuclear pore protein
Chain IDs:QA (auth: J0), RA (auth: J1), SA (auth: J2), TA (auth: J3), UA (auth: J4), VA (auth: J5)
Chain Length:709
Number of Molecules:6
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nucleoporin 133
Chain IDs:WA (auth: K0), XA (auth: K1), YA (auth: K2), ZA (auth: K3)
Chain Length:1206
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nuclear pore complex protein
Chain IDs:AB (auth: L0), BB (auth: L1), CB (auth: L2), DB (auth: L3)
Chain Length:985
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nuclear pore complex protein Nup98-Nup96
Chain IDs:EB (auth: M0), FB (auth: M1), GB (auth: M2), HB (auth: M3)
Chain Length:889
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Protein SEC13 homolog
Chain IDs:IB (auth: N0), JB (auth: N1), KB (auth: N2), LB (auth: N3)
Chain Length:301
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Seh1
Chain IDs:MB (auth: O0), NB (auth: O1), OB (auth: O2), PB (auth: O3)
Chain Length:467
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nuclear pore complex protein nup85
Chain IDs:QB (auth: P0), RB (auth: P1), SB (auth: P2), TB (auth: P3)
Chain Length:890
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nuclear pore complex protein nup43
Chain IDs:UB (auth: Q0), VB (auth: Q1), WB (auth: Q2), XB (auth: Q3)
Chain Length:417
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nup160
Chain IDs:YB (auth: R0), ZB (auth: R1), AC (auth: R2), BC (auth: R3)
Chain Length:1791
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:ELYS-like domain-containing protein
Chain IDs:CC (auth: T0), DC (auth: T1), EC (auth: T2), FC (auth: T3)
Chain Length:2221
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nuclear pore complex protein Nup98-Nup96
Chain IDs:GC (auth: U0), HC (auth: U1), IC (auth: U2), JC (auth: U3)
Chain Length:1164
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:WD40-like domain-containing protein
Chain IDs:KC (auth: V0), LC (auth: V1)
Chain Length:1704
Number of Molecules:2
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nup88
Chain IDs:MC (auth: W0), NC (auth: W1)
Chain Length:961
Number of Molecules:2
Biological Source:Dictyostelium discoideum
Polymer Type:polypeptide(L)
Description:Nup205
Chain IDs:OC (auth: X0), PC (auth: X1), QC (auth: X2), RC (auth: X3)
Chain Length:405
Number of Molecules:4
Biological Source:Dictyostelium discoideum
Ligand Molecules
Primary Citation
Nuclear pore permeability and fluid flow are modulated by its dilation state.
Mol.Cell 85 537 ? (2025)
PMID: 39729993 DOI: 10.1016/j.molcel.2024.11.038

Abstact

Changing environmental conditions necessitate rapid adaptation of cytoplasmic and nuclear volumes. We use the slime mold Dictyostelium discoideum, known for its ability to tolerate extreme changes in osmolarity, to assess which role nuclear pore complexes (NPCs) play in achieving nuclear volume adaptation and relieving mechanical stress. We capitalize on the unique properties of D. discoideum to quantify fluid flow across NPCs. D. discoideum has an elaborate NPC structure in situ. Its dilation state affects NPC permeability for nucleocytosolic flow. Based on mathematical concepts adapted from hydrodynamics, we conceptualize this phenomenon as porous flow across NPCs, which is distinct from canonically characterized modes of nucleocytoplasmic transport because of its dependence on pressure. Viral NPC blockage decreased nucleocytosolic flow. Our results may be relevant for any biological conditions that entail rapid nuclear size adaptation, including metastasizing cancer cells, migrating cells, or differentiating tissues.

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Primary Citation of related structures