2DZO

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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

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

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

To be published.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50086
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33298
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-10-16

Deposition Author(s):

Padmanabhan, B.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.