1N87 | pdb_00001n87

Solution structure of the U-box of Prp19


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 1N87

This is version 1.4 of the entry. See complete history

Literature

Structural insights into the U-box, a domain associated with multi-ubiquitination

Ohi, M.D.Vander Kooi, C.W.Rosenberg, J.A.Chazin, W.J.Gould, K.L.

(2003) Nat Struct Biol 10: 250-255

  • DOI: https://doi.org/10.1038/nsb906
  • Primary Citation Related Structures: 
    1N87

  • PubMed Abstract: 

    The structure of the U-box in the essential Saccharomyces cerevisiae pre-mRNA splicing factor Prp19p has been determined by NMR. The conserved zinc-binding sites supporting the cross-brace arrangement in RING-finger domains are replaced by hydrogen-bonding networks in the U-box. These hydrogen-bonding networks are necessary for the structural stabilization and activity of the U-box. A conservative Val-->Ile point mutation in the Prp19p U-box domain leads to pre-mRNA splicing defects in vivo. NMR analysis of this mutant shows that the substitution disrupts structural integrity of the U-box domain. Furthermore, comparison of the Prp19p U-box domain with known RING-E2 complex structures demonstrates that both U-box and RING-fingers contain a conserved interaction surface. Mutagenesis of residues at this interface, while not perturbing the structure of the U-box, abrogates Prp19p function in vivo. These comparative structural and functional analyses imply that the U-box and its associated ubiquitin ligase activity are critical for Prp19p function in vivo.


  • Organizational Affiliation
    • Howard Hughes Medical Institute School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.

Macromolecule Content 

  • Total Structure Weight: 6.25 kDa 
  • Atom Count: 436 
  • Modeled Residue Count: 56 
  • Deposited Residue Count: 56 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA splicing factor PRP1956Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: Prp19
EC: 2.3.2.27
UniProt
Find proteins for P32523 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32523 
Go to UniProtKB:  P32523
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32523
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-15
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection