8ZZK | pdb_00008zzk

Structure of the S. cerevisiae nuclear pore complex cytoplasmic mRNA export platform, Nup82

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/pdb8ZZK/pdb

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


• Deposited: 2018-06-06 Released: 2018-06-14 
• Deposition Author(s): Fernandez-Martinez, J., Kim, S.J., Shi, Y., Upla, P., Pellarin, R., Gagnon, M., Chemmama, I.E., Wang, J., Nudelman, I., Zhang, W., Williams, R., Rice, W.J., Stokes, D.L., Zenklusen, D., Chait, B.T., Sali, A., Rout, M.P.

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Integrative Structure Snapshot

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

Literature

Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform.

Fernandez-Martinez, J., Kim, S.J., Shi, Y., Upla, P., Pellarin, R., Gagnon, M., Chemmama, I.E., Wang, J., Nudelman, I., Zhang, W., Williams, R., Rice, W.J., Stokes, D.L., Zenklusen, D., Chait, B.T., Sali, A., Rout, M.P.

(2016) Cell 167: 1215-1228.e25

• PubMed: 27839866 
• DOI: https://doi.org/10.1016/j.cell.2016.10.028
• Primary Citation Related Structures: 
  8ZZK


• PubMed Abstract: 
  

  The last steps in mRNA export and remodeling are performed by the Nup82 complex, a large conserved assembly at the cytoplasmic face of the nuclear pore complex (NPC). By integrating diverse structural data, we have determined the molecular architecture of the native Nup82 complex at subnanometer precision. The complex consists of two compositionally identical multiprotein subunits that adopt different configurations. The Nup82 complex fits into the NPC through the outer ring Nup84 complex. Our map shows that this entire 14-MDa Nup82-Nup84 complex assembly positions the cytoplasmic mRNA export factor docking sites and messenger ribonucleoprotein (mRNP) remodeling machinery right over the NPC's central channel rather than on distal cytoplasmic filaments, as previously supposed. We suggest that this configuration efficiently captures and remodels exporting mRNP particles immediately upon reaching the cytoplasmic side of the NPC.

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Organizational Affiliation: 
• Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
Departments of Bioengineering and Therapeutic Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.
Departments of Bioengineering and Therapeutic Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, 75015 Paris, France.
Département de Biochimie et Médecine Moléculaire, University of Montréal, Montréal, QC H3C3J7, Canada.
Simons Electron Microscopy Center at New York Structural Biology Center, New York, NY 10027, USA.
Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA. Electronic address: [e-mail].
Departments of Bioengineering and Therapeutic Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: [e-mail].
Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: [e-mail].

Assembly  

Macromolecule Content 

• Total Structure Weight: 1,060.45 kDa 
• Modeled Residue Count: 8,402 
• Deposited Residue Count: 8,402 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dyn2	A, B	92	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: DYN2
UniProt
Find proteins for Q02647 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02647  Go to UniProtKB:  Q02647

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup82	C, D	713	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NUP82
UniProt
Find proteins for P40368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40368  Go to UniProtKB:  P40368

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup159	E, F	1,460	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NUP159
UniProt
Find proteins for P40477 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40477  Go to UniProtKB:  P40477

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nsp1	G, H	823	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NSP1
UniProt
Find proteins for P14907 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14907  Go to UniProtKB:  P14907

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup116	I, J	1,113	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NUP116
UniProt
Find proteins for Q02630 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02630  Go to UniProtKB:  Q02630

Experimental Data & Validation

Integrative Structure Snapshot

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

Structure Validation

View Full Validation Report

View Summary Validation Report

Entry History 

Deposition Data

• Released Date: 2018-06-14 
Deposition Author(s): Fernandez-Martinez, J., Kim, S.J., Shi, Y., Upla, P., Pellarin, R., Gagnon, M., Chemmama, I.E., Wang, J., Nudelman, I., Zhang, W., Williams, R., Rice, W.J., Stokes, D.L., Zenklusen, D., Chait, B.T., Sali, A., Rout, M.P.

Revision History  

• Version 1.0: 2018-06-14
  Type: Initial release