4B0Z | pdb_00004b0z

Crystal structure of S. pombe Rpn12

• PDB DOI: https://doi.org/10.2210/pdb4B0Z/pdb

• Classification: PROTEIN BINDING
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-06 Released: 2012-09-12 
• Deposition Author(s): Boehringer, J., Riedinger, C., Paraskevopoulos, K., Johnson, E.O.D., Lowe, E.D., Khoudian, C., Smith, D., Noble, M.E.M., Gordon, C., Endicott, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.225 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Structural and Functional Characterisation of Rpn12 Identifies Residues Required for Rpn10 Proteasome Incorporation.

Boehringer, J., Riedinger, C., Paraskevopoulos, K., Johnson, E.O.D., Lowe, E.D., Khoudian, C., Smith, D., Noble, M.E.M., Gordon, C., Endicott, J.A.

(2012) Biochem J 448: 55

• PubMed: 22906049 
• DOI: https://doi.org/10.1042/BJ20120542
• Primary Citation Related Structures: 
  4B0Z


• PubMed Abstract: 
  

  The ubiquitin-proteasome system targets selected proteins for degradation by the 26S proteasome. Rpn12 is an essential component of the 19S regulatory particle and plays a role in recruiting the extrinsic ubiquitin receptor Rpn10. In the present paper we report the crystal structure of Rpn12, a proteasomal PCI-domain-containing protein. The structure helps to define a core structural motif for the PCI domain and identifies potential sites through which Rpn12 might form protein-protein interactions. We demonstrate that mutating residues at one of these sites impairs Rpn12 binding to Rpn10 in vitro and reduces Rpn10 incorporation into proteasomes in vivo.

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Organizational Affiliation: 
• Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 53.19 kDa 
• Atom Count: 4,154 
• Modeled Residue Count: 447 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S PROTEASOME REGULATORY SUBUNIT RPN12	A, B	229	Schizosaccharomyces pombe	Mutation(s): 0
UniProt
Find proteins for P50524 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P50524  Go to UniProtKB:  P50524

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SGM	F [auth A], H [auth B]	MONOTHIOGLYCEROL C3 H8 O2 S PJUIMOJAAPLTRJ-GSVOUGTGSA-N
GOL	I [auth B], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3	C [auth A], D [auth A], E [auth A], G [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.225 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.78	α = 90
b = 91.38	β = 90
c = 143.34	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Boehringer, J., Riedinger, C., Paraskevopoulos, K., Johnson, E.O.D., Lowe, E.D., Khoudian, C., Smith, D., Noble, M.E.M., Gordon, C., Endicott, J.A.

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2012-11-07
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary