9A3S | pdb_00009a3s

Implications of a multiscale structure of the yeast Nuclear Pore Complex

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.

• PDB DOI: https://doi.org/10.2210/pdb9A3S/pdb

• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Mutation(s): No 


• Deposited: 2023-08-25 Released: 2024-05-10 
• Deposition Author(s): Akey, C.A., Echeverria, I., Ouch, C., Nudelman, I., Shi, Y., Wang, J., Weiss, T.M., Chait, B.T., Sali, A., Fernandez-Martinez, J., Rout, M.P.

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Integrative Structure Snapshot

• Multi-Scale: Yes 
• Multi-State: No 
• Ordered-State: No 
• Deposited Models: 11 
• Representative Model: 1 

Literature

Implications of a multiscale structure of the yeast Nuclear Pore Complex

Akey, C.A., Echeverria, I., Ouch, C., Nudelman, I., Shi, Y., Wang, J., Weiss, T.M., Shi, Y., Chait, B.T., Sali, A., Fernandez-Martinez, J., Rout, M.P.

(2023) Molecular Cell 83: 3283-3302

• PubMed: 37738963 
• DOI: https://doi.org/10.1016/j.molcel.2023.08.025
• Primary Citation of Related Structures:  
  8T9L, 8TIE, 8TJ5, 9A3S


• PubMed Abstract: 
  

  Nuclear pore complexes (NPCs) direct the nucleocytoplasmic transport of macromolecules. Here, we provide a composite multiscale structure of the yeast NPC, based on improved 3D density maps from cryogenic electron microscopy and AlphaFold2 models. Key features of the inner and outer rings were integrated into a comprehensive model. We resolved flexible connectors that tie together the core scaffold, along with equatorial transmembrane complexes and a lumenal ring that anchor this channel within the pore membrane. The organization of the nuclear double outer ring reveals an architecture that may be shared with ancestral NPCs. Additional connections between the core scaffold and the central transporter suggest that under certain conditions, a degree of local organization is present at the periphery of the transport machinery. These connectors may couple conformational changes in the scaffold to the central transporter to modulate transport. Collectively, this analysis provides insights into assembly, transport, and NPC evolution.

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Organizational Affiliation: 
• Department of Pharmacology, Physiology and Biophysics, Boston University, Chobanian and Avedisian School of Medicine, 700 Albany Street, Boston, MA 02118, USA. Electronic address: [e-mail].
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
Department of Pharmacology, Physiology and Biophysics, Boston University, Chobanian and Avedisian School of Medicine, 700 Albany Street, Boston, MA 02118, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605, USA.
Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA.
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain.
Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: [e-mail].

Assembly  

Macromolecule Content 

• Total Structure Weight: 431.11 kDa 
• Modeled Residue Count: 3,272 
• Deposited Residue Count: 3,272 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoporin POM152	A, B	1,337	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: POM152
UniProt
Find proteins for P39685 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39685  Go to UniProtKB:  P39685

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoporin POM34	C, D	299	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: POM34
UniProt
Find proteins for Q12445 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12445  Go to UniProtKB:  Q12445

Experimental Data & Validation

Integrative Structure Snapshot

• Multi-Scale: Yes 
• Multi-State: No 
• Ordered-State: No 
• Deposited Models: 11 
• Representative Model: 1 

Structure Validation

View Full Validation Report

View Summary Validation Report

Entry History 

Deposition Data

• Released Date: 2024-05-10 
Deposition Author(s): Akey, C.A., Echeverria, I., Ouch, C., Nudelman, I., Shi, Y., Wang, J., Weiss, T.M., Chait, B.T., Sali, A., Fernandez-Martinez, J., Rout, M.P.

Revision History  

• Version 1.0: 2024-05-10
  Type: Initial release