1OI0 | pdb_00001oi0

CRYSTAL STRUCTURE OF AF2198, A JAB1/MPN DOMAIN PROTEIN FROM ARCHAEOGLOBUS FULGIDUS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.242 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history. 

Literature

The Structure of the Jab1/Mpn Domain and its Implications for Proteasome Function

Tran, H.J.T.T., Allen, M.D., Lowe, J., Bycroft, M.

(2003) Biochemistry 42: 11460

  • DOI: https://doi.org/10.1021/bi035033g
  • Primary Citation Related Structures: 
    1OI0

  • PubMed Abstract: 

    The 26S proteasome is responsible for the degradation of polyubiquitinated proteins. During this process the polyubiquitin chain is removed. The identity of the proteasomal component that is responsible for this activity has not been clear, as it contains no subunits that resemble known deubiquitinating enzymes. The Jab1/MPN domain is a widespread 120 amino acid protein module found in archaea, bacteria, and eukaryotes. In eukaryotes the Jab1/MPN domain is found in subunits of several multiprotein complexes including the proteasome. Recently it has been proposed that the Jab1/MPN domain of the proteasomal subunit Rpn11 is responsible for the removal of the polyubiquitin chain from substrate proteins. Here we report the crystal structure and characterization of AF2198, a Jab1/MPN domain protein from Archaeoglobolus fulgidus. The structure reveals a fold that resembles that of cytidine deaminase and places the Jab1/MPN domain in a superfamily of metal dependent hydrolases.

    • Organizational Affiliation: 
    • MRC Centre for Protein Engineering, Cambridge CB2 2QH, U.K.

Macromolecule Content 

  • Total Structure Weight: 55.97 kDa 
  • Atom Count: 3,679 
  • Modeled Residue Count: 426 
  • Deposited Residue Count: 496 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HYPOTHETICAL PROTEIN AF2198
A, B, C, D
124Archaeoglobus fulgidusMutation(s): 0 
UniProt
Find proteins for O28085 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O28085 
Go to UniProtKB:  O28085
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28085
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.242 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.787α = 90
b = 87.081β = 94
c = 67.827γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary