3VR0

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.237
R-Value Work: 0.196
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0060294
Primary Citation of 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8U1R3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AU Query on AU Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth B] 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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.237
R-Value Work: 0.196
R-Value Observed: 0.198
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-04-03

Deposition Author(s):

Revision History (Full details and data files)

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