2DZO | pdb_00002dzo

Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3

• PDB DOI: https://doi.org/10.2210/pdb2DZO/pdb

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


• Deposited: 2006-09-29 Released: 2007-10-16 
• Deposition Author(s): Nakamura, Y., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.282 (Depositor) 
• R-Value Work: 
  0.212 (Depositor) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3

Nakamura, Y., Padmanabhan, B., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 69.71 kDa 
• Atom Count: 4,763 
• Modelled Residue Count: 579 
• Deposited Residue Count: 620 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable 26S proteasome regulatory subunit p28	A, C	228	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P50086 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P50086  Go to UniProtKB:  P50086

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 6B homolog	B, D	82	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P33298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33298  Go to UniProtKB:  P33298

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.282 (Depositor) 
• R-Value Work:  0.212 (Depositor) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.599	α = 90
b = 99.599	β = 90
c = 73.082	γ = 120

Software Package:

Software Name	Purpose
MOLREP	phasing
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-16 
Deposition Author(s): Nakamura, Y., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description