5M88

Spliceosome component


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

Starting Model: other
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Prp19/Pso4 Is an Autoinhibited Ubiquitin Ligase Activated by Stepwise Assembly of Three Splicing Factors.

de Moura, T.R.Mozaffari-Jovin, S.Szabo, C.Z.K.Schmitzova, J.Dybkov, O.Cretu, C.Kachala, M.Svergun, D.Urlaub, H.Luhrmann, R.Pena, V.

(2018) Mol Cell 69: 979-992.e6

  • DOI: https://doi.org/10.1016/j.molcel.2018.02.022
  • Primary Citation of Related Structures:  
    5M88, 5M89, 5M8C

  • PubMed Abstract: 

    Human nineteen complex (NTC) acts as a multimeric E3 ubiquitin ligase in DNA repair and splicing. The transfer of ubiquitin is mediated by Prp19-a homotetrameric component of NTC whose elongated coiled coils serve as an assembly axis for two other proteins called SPF27 and CDC5L. We find that Prp19 is inactive on its own and have elucidated the structural basis of its autoinhibition by crystallography and mutational analysis. Formation of the NTC core by stepwise assembly of SPF27, CDC5L, and PLRG1 onto the Prp19 tetramer enables ubiquitin ligation. Protein-protein crosslinking of NTC, functional assays in vitro, and assessment of its role in DNA damage response provide mechanistic insight into the organization of the NTC core and the communication between PLRG1 and Prp19 that enables E3 activity. This reveals a unique mode of regulation for a complex E3 ligase and advances understanding of its dynamics in various cellular pathways.


  • Organizational Affiliation

    Macromolecular Crystallography Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Core
A, B
136Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0072540
EC: 2.3.2.27
UniProt
Find proteins for G0SFY0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SFY0 
Go to UniProtKB:  G0SFY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SFY0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.867α = 90
b = 103.013β = 92.59
c = 94.105γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Database references
  • Version 1.2: 2018-03-28
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description