Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Nuclear pore permeability and fluid flow are modulated by its dilation state.
Journal, issue, pages	Mol Cell, Vol. 85, Issue 3, Page 537-554.e11, Year 2025
Publish date	Feb 6, 2025
Authors	Patrick C Hoffmann / Hyuntae Kim / Agnieszka Obarska-Kosinska / Jan Philipp Kreysing / Eli Andino-Frydman / Sergio Cruz-León / Erica Margiotta / Lenka Cernikova / Jan Kosinski / Beata Turoňová / Gerhard Hummer / Martin Beck /
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 ...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.
External links	Mol Cell / PubMed:39729993
Methods	EM (subtomogram averaging) / EM (tomography)
Resolution	4.5 - 40.0 Å
Structure data	19137 9hcj EMDB-19137: Composite structure of the Dictyostelium discoideum nuclear pore complex in cells PDB-9hcj: D. discoideum nuclear pore complex Method: EM (subtomogram averaging) / Resolution: 30.0 Å EMDB-19139: Asymmetric subunit of the Dictyostelium discoideum nuclear pore complex Method: EM (subtomogram averaging) / Resolution: 36.0 Å EMDB-19140: Inner ring segment of the Dictyostelium discoideum nuclear pore complex Method: EM (subtomogram averaging) / Resolution: 25.0 Å EMDB-19141: Cytoplasmic ring segment of the Dictyostelium discoideum nuclear pore complex Method: EM (subtomogram averaging) / Resolution: 26.0 Å EMDB-19142: Nuclear ring segment of the Dictyostelium discoideum nuclear pore complex Method: EM (subtomogram averaging) / Resolution: 23.0 Å EMDB-19143: Lumenal ring segment of the Dictyostelium discoideum nuclear pore complex Method: EM (subtomogram averaging) / Resolution: 27.0 Å EMDB-19144: Nuclear ring segment focused around the basket connection of the Dictyostelium discoideum nuclear pore complex Method: EM (subtomogram averaging) / Resolution: 24.0 Å EMDB-19149: Composite structure of the Dictyostelium discoideum nuclear pore complex in cells - control condition Method: EM (subtomogram averaging) / Resolution: 33.0 Å EMDB-19152: Asymmetric subunit of the Dictyostelium discoideum nuclear pore complex - control condition Method: EM (subtomogram averaging) / Resolution: 33.0 Å EMDB-19155: Composite structure of the Dictyostelium discoideum nuclear pore complex in cells - hyperosmotic stress Method: EM (subtomogram averaging) / Resolution: 38.0 Å EMDB-19156: Asymmetric subunit of the Dictyostelium discoideum nuclear pore complex - hyperosmotic stress Method: EM (subtomogram averaging) / Resolution: 38.0 Å EMDB-19157: Composite structure of the Dictyostelium discoideum nuclear pore complex in cells - hypoosmotic stress Method: EM (subtomogram averaging) / Resolution: 37.0 Å EMDB-19158: Asymmetric subunit of the Dictyostelium discoideum nuclear pore complex - hypoosmotic stress Method: EM (subtomogram averaging) / Resolution: 37.0 Å EMDB-51989: Inner ring segment of the Dictyostelium discoideum NPC - control condition Method: EM (subtomogram averaging) / Resolution: 33.0 Å EMDB-51990: Cytoplasmic ring segment of the Dictyostelium discoideum NPC - control condition Method: EM (subtomogram averaging) / Resolution: 33.0 Å EMDB-51991: Nuclear ring segment of the Dictyostelium discoideum NPC - control condition Method: EM (subtomogram averaging) / Resolution: 33.0 Å EMDB-51992: Lumenal ring segment of the Dictyostelium discoideum NPC - control condition Method: EM (subtomogram averaging) / Resolution: 33.0 Å EMDB-51993: Nuclear ring segment focused around the basket connection of the Dictyostelium discoideum NPC - control condition Method: EM (subtomogram averaging) / Resolution: 33.0 Å EMDB-51994: Inner ring segment of the Dictyostelium discoideum NPC - hyperosmotic stress Method: EM (subtomogram averaging) / Resolution: 38.0 Å EMDB-51995: Cytoplasmic ring segment of the Dictyostelium discoideum NPC - hyperosmotic stress Method: EM (subtomogram averaging) / Resolution: 38.0 Å EMDB-51996: Nuclear ring segment of the Dictyostelium discoideum NPC - hyperosmotic stress Method: EM (subtomogram averaging) / Resolution: 38.0 Å EMDB-51997: Lumenal ring segment of the Dictyostelium discoideum NPC - hyperosmotic stress Method: EM (subtomogram averaging) / Resolution: 38.0 Å EMDB-51998: Nuclear ring segment focused around the basket connection of the Dictyostelium discoideum NPC - hyperosmotic stress Method: EM (subtomogram averaging) / Resolution: 38.0 Å EMDB-51999: Inner ring segment of the Dictyostelium discoideum NPC - hypoosmotic stress Method: EM (subtomogram averaging) / Resolution: 40.0 Å EMDB-52000: Cytoplasmic ring segment of the Dictyostelium discoideum NPC - hypoosmotic stress Method: EM (subtomogram averaging) / Resolution: 40.0 Å EMDB-52001: Nuclear ring segment of the Dictyostelium discoideum NPC - hypoosmotic stress Method: EM (subtomogram averaging) / Resolution: 40.0 Å EMDB-52002: Lumenal ring segment of the Dictyostelium discoideum NPC - hypoosmotic stress Method: EM (subtomogram averaging) / Resolution: 40.0 Å EMDB-52003: Nuclear ring segment focused around the basket connection of the Dictyostelium discoideum NPC - hypoosmotic stress Method: EM (subtomogram averaging) / Resolution: 40.0 Å EMDB-52053: Cryo-tomogram of Dictyostelium discoideum cell - control condition (HL5), related to Figure 1b Method: EM (tomography) EMDB-52054: Cryo-tomogram of Dictyostelium discoideum cell - hyperosmotic stress condition (+0.4 M sorbitol), related to Figure 1b Method: EM (tomography) EMDB-52055: Cryo-tomogram of Dictyostelium discoideum cell - hypoosmotic stress condition (distilled water), related to Figure 1b Method: EM (tomography) EMDB-52057: In situ Dictyostelium discoideum 80S ribosome - hyperosmotic stress condition Method: EM (subtomogram averaging) / Resolution: 4.5 Å EMDB-52058: In situ Dictyostelium discoideum 80S ribosome - hypoosmotic stress condition Method: EM (subtomogram averaging) / Resolution: 5.9 Å
Source	Dictyostelium discoideum AX2 (eukaryote) dictyostelium discoideum (eukaryote)
Keywords	NUCLEAR PROTEIN / Nuclear pore complex