4O06 | pdb_00004o06

1.15A Resolution Structure of the Proteasome Assembly Chaperone Nas2 PDZ Domain

• PDB DOI: https://doi.org/10.2210/pdb4O06/pdb

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


• Deposited: 2013-12-13 Released: 2014-04-16 
• Deposition Author(s): Lovell, S., Mehzabeen, N., Battaile, K.P., Singh, C.R., Chowdhury, W.Q., Geanes, E., Roelofs, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.194 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

1.15 angstrom resolution structure of the proteasome-assembly chaperone Nas2 PDZ domain.

Singh, C.R., Lovell, S., Mehzabeen, N., Chowdhury, W.Q., Geanes, E.S., Battaile, K.P., Roelofs, J.

(2014) Acta Crystallogr F Struct Biol Commun 70: 418-423

• PubMed: 24699731 
• DOI: https://doi.org/10.1107/S2053230X14003884
• Primary Citation Related Structures: 
  4O06


• PubMed Abstract: 
  

  The 26S proteasome is a 2.5 MDa protease dedicated to the degradation of ubiquitinated proteins in eukaryotes. The assembly of this complex containing 66 polypeptides is assisted by at least nine proteasome-specific chaperones. One of these, Nas2, binds to the proteasomal AAA-ATPase subunit Rpt5. The PDZ domain of Nas2 binds to the C-terminal tail of Rpt5; however, it does not require the C-terminus of Rpt5 for binding. Here, the 1.15 Å resolution structure of the PDZ domain of Nas2 is reported. This structure will provide a basis for further insights regarding the structure and function of Nas2 in proteasome assembly.

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Organizational Affiliation: 
• Division of Biology, Kansas State University, 338 Ackert Hall, Manhattan, KS 66506, USA.
Protein Structure Laboratory, University of Kansas, Del Shankel Structural Biology Center, Lawrence, KS 66047, USA.
IMCA-CAT Hauptman-Woodward Medical Research Institute, 9700 South Cass Avenue, Building 435A, Argonne, IL 60439, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 11.93 kDa 
• Atom Count: 915 
• Modeled Residue Count: 102 
• Deposited Residue Count: 106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable 26S proteasome regulatory subunit p27	A	106	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: NAS2, YIL007C
UniProt
Find proteins for P40555 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40555  Go to UniProtKB:  P40555

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.194 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.968	α = 90
b = 39.968	β = 90
c = 115.827	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XSCALE	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-16 
Deposition Author(s): Lovell, S., Mehzabeen, N., Battaile, K.P., Singh, C.R., Chowdhury, W.Q., Geanes, E., Roelofs, J.

Revision History  

• Version 1.0: 2014-04-16
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description