9A0H | pdb_00009a0h

Integrative model of Nup116 knockout (at 37C) 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/pdb9A0H/pdb

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


• Deposited: 2020-06-04 Released: 2020-08-28 
• Deposition Author(s): Vasileios Rantos, Matteo Allegretti, Christian E. Zimmerli, Florian Wilfling, Paolo Ronchi, Herman K.H. Fung, Chia-Wei Lee, Wim Hagen, Beata Turonova, Kai Karius, Mandy Boermel, Xiaojie Zhang, Christoph Mueller, Yannick Schwab, Julia Mahamid, Boris Pfander, Martin Beck, Jan Kosinski

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Integrative Structure Snapshot

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

Literature

In cell architecture of the nuclear pore and snapshots of its turnover

Matteo Allegretti, Christian E. Zimmerli, Vasileios Rantos, Florian Wilfling, Paolo Ronchi, Herman K.H. Fung, Chia-Wei Lee, Wim Hagen, Beata Turonova, Kai Karius, Mandy Boermel, Xiaojie Zhang, Christoph Mueller, Yannick Schwab, Julia Mahamid, Boris Pfander, Jan Kosinski, Martin Beck

(2020) Nature 0: 0-0

• DOI: https://doi.org/10.1038/s41586-020-2670-5

Assembly  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A1B1C1D1E1F1G1H1I1J1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A2B1C1D1E1F1G1H1I1 

Macromolecule Content 

• Total Structure Weight: 1,178.28 kDa 
• Atom Count: 57,495 
• Modeled Residue Count: 8,907 
• Deposited Residue Count: 8,907 
• Unique protein chains: 10

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nic96	A1	839	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NIC96
UniProt
Find proteins for P34077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34077  Go to UniProtKB:  P34077

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup188	B1	1,655	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NUP188
UniProt
Find proteins for P52593 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P52593  Go to UniProtKB:  P52593

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup157	D1	1,391	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NUP157
UniProt
Find proteins for P40064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40064  Go to UniProtKB:  P40064

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup133	K1	1,157	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NUP133
UniProt
Find proteins for P36161 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36161  Go to UniProtKB:  P36161

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup84	L1	726	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NUP84
UniProt
Find proteins for P52891 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P52891  Go to UniProtKB:  P52891

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup145c	M1	712	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NUP145 EC: 3.4.21
UniProt
Find proteins for P49687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49687  Go to UniProtKB:  P49687

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Sec13	N1	297	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: SEC13
UniProt
Find proteins for Q04491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04491  Go to UniProtKB:  Q04491

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Seh1	O1	349	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: SEH1
UniProt
Find proteins for P53011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53011  Go to UniProtKB:  P53011

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup85	P1	744	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NUP85
UniProt
Find proteins for P46673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P46673  Go to UniProtKB:  P46673

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Nup120	R1	1,037	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NUP120
UniProt
Find proteins for P35729 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35729  Go to UniProtKB:  P35729

Experimental Data & Validation

Integrative Structure Snapshot

• Multi-Scale: No 
• 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: 2020-08-28 
Deposition Author(s): Vasileios Rantos, Matteo Allegretti, Christian E. Zimmerli, Florian Wilfling, Paolo Ronchi, Herman K.H. Fung, Chia-Wei Lee, Wim Hagen, Beata Turonova, Kai Karius, Mandy Boermel, Xiaojie Zhang, Christoph Mueller, Yannick Schwab, Julia Mahamid, Boris Pfander, Martin Beck, Jan Kosinski

Revision History  

• Version 1.0: 2020-08-28
  Type: Initial release