5UAZ | pdb_00005uaz

Crystal structure of the yeast nucleoporin

• PDB DOI: https://doi.org/10.2210/pdb5UAZ/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-20 Released: 2017-12-27 
• Deposition Author(s): Blus, B.J., Blobel, G.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the yeast nucleoporin

Blus, B.J., Blobel, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.96 kDa 
• Atom Count: 1,652 
• Modeled Residue Count: 188 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoporin NUP53	A, B	111	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: NUP53, YMR153W, YM8520.02
UniProt
Find proteins for Q03790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03790  Go to UniProtKB:  Q03790

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth B], D [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.497	α = 90
b = 100.487	β = 90
c = 85.225	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Blus, B.J., Blobel, G.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description