6X03 | pdb_00006x03

Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 and VHH-SAN9

• PDB DOI: https://doi.org/10.2210/pdb6X03/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C, Vicugna pacos
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-15 Released: 2020-12-09 
• Deposition Author(s): Nordeen, S.A., Schwartz, T.U.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 7.30 Å
• R-Value Free: 
  0.353 (Depositor), 0.354 (DCC) 
• R-Value Work: 
  0.335 (Depositor), 0.335 (DCC) 
• R-Value Observed: 
  0.337 (Depositor) 

Starting Model: other

Literature

Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif.

Nordeen, S.A., Turman, D.L., Schwartz, T.U.

(2020) Nat Commun 11: 6060-6060

• PubMed: 33247142 
• DOI: https://doi.org/10.1038/s41467-020-19885-5
• Primary Citation Related Structures: 
  6X02, 6X03, 6X04, 6X05


• PubMed Abstract: 
  

  The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus occurs through the nuclear pore complex (NPC). The heptameric Nup84 or Y complex is an essential scaffolding component of the NPC. Here we report two nanobody-bound structures: the full-length Nup84-Nup133 C-terminal domain complex and the Nup133 N-terminal domain, both from S. cerevisiae. Together with previously published structures, this work enables the structural description of the entire 575 kDa Y complex from one species. The structure of Nup84-Nup133 _CTD details the high flexibility of this dimeric unit of the Y complex. Further, the Nup133 _NTD contains a structurally conserved amphipathic lipid packing sensor motif, confirmed by liposome interaction studies. The presented structures reveal important details about the function of the Y complex that affect our understanding of NPC structure and assembly.

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Organizational Affiliation: 
• Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 186.71 kDa 
• Atom Count: 7,091 
• Modeled Residue Count: 1,429 
• Deposited Residue Count: 1,628 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoporin NUP84	A	726	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: NUP84, YDL116W
UniProt
Find proteins for P52891 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P52891  Go to UniProtKB:  P52891

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoporin NUP133	B	643	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: NUP133, RAT3, YKR082W, YKR402
UniProt
Find proteins for P36161 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36161  Go to UniProtKB:  P36161

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH-SAN8	C	131	Vicugna pacos	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH-SAN9	D	128	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 7.30 Å
• R-Value Free:  0.353 (Depositor), 0.354 (DCC) 
• R-Value Work:  0.335 (Depositor), 0.335 (DCC) 
• R-Value Observed: 0.337 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.252	α = 90
b = 295.205	β = 90
c = 295.609	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Nordeen, S.A., Schwartz, T.U.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM077537

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Data collection, Database references, Other
• Version 1.2: 2024-04-03
  Changes: Refinement description