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 3HIB | pdb_00003hib

Crystal structure of the second Sec63 domain of yeast Brr2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.257 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

wwPDB Validation 3D Report Full Report

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

Literature

Structural evidence for consecutive Hel308-like modules in the spliceosomal ATPase Brr2.

Zhang, L., Xu, T., Maeder, C., Bud, L.O., Shanks, J., Nix, J., Guthrie, C., Pleiss, J.A., Zhao, R.

(2009) Nat Struct Mol Biol 16: 731-739

  • DOI: https://doi.org/10.1038/nsmb.1625
  • Primary Citation Related Structures: 
    3HIB

  • PubMed Abstract: 

    Brr2 is a DExD/H-box helicase responsible for U4/U6 unwinding during spliceosomal activation. Brr2 contains two helicase-like domains, each of which is followed by a Sec63 domain with unknown function. We determined the crystal structure of the second Sec63 domain, which unexpectedly resembles domains 4 and 5 of DNA helicase Hel308. This, together with sequence similarities between Brr2's helicase-like domains and domains 1-3 of Hel308, led us to hypothesize that Brr2 contains two consecutive Hel308-like modules (Hel308-I and Hel308-II). Our structural model and mutagenesis data suggest that Brr2 shares a similar helicase mechanism with Hel308. We demonstrate that Hel308-II interacts with Prp8 and Snu114 in vitro and in vivo. We further find that the C-terminal region of Prp8 (Prp8-CTR) facilitates the binding of the Brr2-Prp8-CTR complex to U4/U6. Our results have important implications for the mechanism and regulation of Brr2's activity in splicing.


  • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA.

Macromolecule Content 

  • Total Structure Weight: 36.28 kDa 
  • Atom Count: 2,674 
  • Modeled Residue Count: 310 
  • Deposited Residue Count: 318 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing helicase BRR2318Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: BRR2, RSS1, SNU246, SYGP-ORF66, YER172C
EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32639 
Go to UniProtKB:  P32639
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32639
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.257 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.153α = 90
b = 75.678β = 90
c = 83.955γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
SOLVEphasing
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary