4OWP | pdb_00004owp

Crystal structure of rpn11 in a heterodimer complex with rpn8, representing the active portion of the proteasome lid.

• PDB DOI: https://doi.org/10.2210/pdb4OWP/pdb

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


• Deposited: 2014-02-03 Released: 2015-08-05 
• Deposition Author(s): Yu, Z., Mansour, W., Nakasone, M.A., Glickman, M.H., Dvir, H.
• Funding Organization(s): Marie Curie, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.242 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal structure of rpn11 in a heterodimer complex with rpn8, representing the active portion of the proteasome lid.In preparation.

Yu, Z., Mansour, W., Nakasone, M.A., Pick, E., Glickman, M.H., Dvir, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 47.88 kDa 
• Atom Count: 2,804 
• Modeled Residue Count: 336 
• Deposited Residue Count: 425 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN8	A	186	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: O5360, RPN8, YOR261C
UniProt
Find proteins for Q08723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08723  Go to UniProtKB:  Q08723

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN11	B	239	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: MPR1, RPN11, YFR004W EC: 3.4.19.12
UniProt
Find proteins for P43588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43588  Go to UniProtKB:  P43588

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.242 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.388	α = 90
b = 70.388	β = 90
c = 199.648	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PDB_EXTRACT	data extraction
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-08-05 
Deposition Author(s): Yu, Z., Mansour, W., Nakasone, M.A., Glickman, M.H., Dvir, H.

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Funding Organization	Location	Grant Number
Marie Curie	Israel	330879
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM095755

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.2: 2019-12-18
  Changes: Database references, Structure summary
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references