9HCJ | pdb_00009hcj

D. discoideum nuclear pore complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 30.0 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Nuclear pore permeability and fluid flow are modulated by its dilation state.

Hoffmann, P.C.Kim, H.Obarska-Kosinska, A.Kreysing, J.P.Andino-Frydman, E.Cruz-Leon, S.Margiotta, E.Cernikova, L.Kosinski, J.Turonova, B.Hummer, G.Beck, M.

(2025) Mol Cell 85: 537

  • DOI: https://doi.org/10.1016/j.molcel.2024.11.038
  • Primary Citation of Related Structures:  
    9HCJ

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RanBP2-type zinc fingerA [auth 00],
B [auth 01]
3,566Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for C7FZW3 (Dictyostelium discoideum)
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UniProt GroupC7FZW3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin 2101,916Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54IS9 (Dictyostelium discoideum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
WD40 repeat-containing proteinK [auth 40],
L [auth 41]
471Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q7KWY3 (Dictyostelium discoideum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore protein979Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q55GW5 (Dictyostelium discoideum)
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UniProt GroupQ55GW5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Nup188S [auth B0],
T [auth B1]
2,174Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54HL2 (Dictyostelium discoideum)
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UniProt GroupQ54HL2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nup205U [auth C0],
V [auth C1],
W [auth C2],
X [auth C3]
1,916Dictyostelium discoideumMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin 155AA [auth D2],
BA [auth D3],
Y [auth D0],
Z [auth D1]
1,575Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54F20 (Dictyostelium discoideum)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NDC1CA [auth E0],
DA [auth E1]
667Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q550C4 (Dictyostelium discoideum)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Nup35EA [auth F0],
FA [auth F1],
GA [auth F2],
HA [auth F3]
95Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q75JH1 (Dictyostelium discoideum)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein nup54IA [auth H0],
JA [auth H1],
KA [auth H2],
LA [auth H3]
440Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q55BX5 (Dictyostelium discoideum)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Nup58MA [auth I0],
NA [auth I1],
OA [auth I2],
PA [auth I3]
581Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54XC5 (Dictyostelium discoideum)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore protein709Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q86IX4 (Dictyostelium discoideum)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin 133WA [auth K0],
XA [auth K1],
YA [auth K2],
ZA [auth K3]
1,206Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54KA3 (Dictyostelium discoideum)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex proteinAB [auth L0],
BB [auth L1],
CB [auth L2],
DB [auth L3]
985Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54N06 (Dictyostelium discoideum)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup98-Nup96EB [auth M0],
FB [auth M1],
GB [auth M2],
HB [auth M3]
889Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54EQ8 (Dictyostelium discoideum)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SEC13 homologIB [auth N0],
JB [auth N1],
KB [auth N2],
LB [auth N3]
301Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54DS8 (Dictyostelium discoideum)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Seh1MB [auth O0],
NB [auth O1],
OB [auth O2],
PB [auth O3]
467Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q86K39 (Dictyostelium discoideum)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein nup85QB [auth P0],
RB [auth P1],
SB [auth P2],
TB [auth P3]
890Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54NA0 (Dictyostelium discoideum)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein nup43UB [auth Q0],
VB [auth Q1],
WB [auth Q2],
XB [auth Q3]
417Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54Z22 (Dictyostelium discoideum)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Nup160AC [auth R2],
BC [auth R3],
YB [auth R0],
ZB [auth R1]
1,791Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q55DW5 (Dictyostelium discoideum)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ELYS-like domain-containing proteinCC [auth T0],
DC [auth T1],
EC [auth T2],
FC [auth T3]
2,221Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q55DZ3 (Dictyostelium discoideum)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup98-Nup96GC [auth U0],
HC [auth U1],
IC [auth U2],
JC [auth U3]
1,164Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54EQ8 (Dictyostelium discoideum)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
WD40-like domain-containing proteinKC [auth V0],
LC [auth V1]
1,704Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54H52 (Dictyostelium discoideum)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Nup88MC [auth W0],
NC [auth W1]
961Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q54XC9 (Dictyostelium discoideum)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Nup205OC [auth X0],
PC [auth X1],
QC [auth X2],
RC [auth X3]
405Dictyostelium discoideumMutation(s): 0 
UniProt
Find proteins for Q556V6 (Dictyostelium discoideum)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 30.0 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101054823
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanyCRC 1507, Project 17
European Molecular Biology Organization (EMBO)European UnionALTF 33-2021

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-01-08
    Changes: Database references
  • Version 1.2: 2025-02-19
    Changes: Database references, Derived calculations