3VR0 | pdb_00003vr0

Crystal structure of Pyrococcus furiosus PbaB, an archaeal proteasome activator

• PDB DOI: https://doi.org/10.2210/pdb3VR0/pdb

• Classification: PROTEIN BINDING
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-02 Released: 2013-04-03 
• Deposition Author(s): Kumoi, K., Satoh, T., Hiromoto, T., Mizushima, T., Kamiya, Y., Noda, M., Uchiyama, S., Murata, K., Yagi, H., Kato, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.237 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

An archaeal homolog of proteasome assembly factor functions as a proteasome activator

Kumoi, K., Satoh, T., Murata, K., Hiromoto, T., Mizushima, T., Kamiya, Y., Noda, M., Uchiyama, S., Yagi, H., Kato, K.

(2013) PLoS One 8: e60294-e60294

• PubMed: 23555947 
• DOI: https://doi.org/10.1371/journal.pone.0060294
• Primary Citation Related Structures: 
  3VR0


• PubMed Abstract: 
  

  Assembly of the eukaryotic 20S proteasome is an ordered process involving several proteins operating as proteasome assembly factors including PAC1-PAC2 but archaeal 20S proteasome subunits can spontaneously assemble into an active cylindrical architecture. Recent bioinformatic analysis identified archaeal PAC1-PAC2 homologs PbaA and PbaB. However, it remains unclear whether such assembly factor-like proteins play an indispensable role in orchestration of proteasome subunits in archaea. We revealed that PbaB forms a homotetramer and exerts a dual function as an ATP-independent proteasome activator and a molecular chaperone through its tentacle-like C-terminal segments. Our findings provide insights into molecular evolution relationships between proteasome activators and assembly factors.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku Nagoya, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 130.68 kDa 
• Atom Count: 8,076 
• Modeled Residue Count: 984 
• Deposited Residue Count: 1,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B, C, D	283	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF1142
UniProt
Find proteins for Q8U1R3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U1R3  Go to UniProtKB:  Q8U1R3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth D], S [auth D], T [auth D], U [auth D], V [auth D]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.237 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.6	α = 90
b = 156.4	β = 90
c = 153	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Kumoi, K., Satoh, T., Hiromoto, T., Mizushima, T., Kamiya, Y., Noda, M., Uchiyama, S., Murata, K., Yagi, H., Kato, K.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2013-07-31
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations