5LSB | pdb_00005lsb

Crystal structure of yeast Hsh49p in complex with Cus1p binding domain.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.233 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Crystal structure of U2 snRNP SF3b components: Hsh49p in complex with Cus1p-binding domain.

van Roon, A.M.Oubridge, C.Obayashi, E.Sposito, B.Newman, A.J.Seraphin, B.Nagai, K.

(2017) RNA 23: 968-981

  • DOI: https://doi.org/10.1261/rna.059378.116
  • Primary Citation Related Structures: 
    5LSB, 5LSL

  • PubMed Abstract: 

    Spliceosomal proteins Hsh49p and Cus1p are components of SF3b, which together with SF3a, Msl1p/Lea1p, Sm proteins, and U2 snRNA, form U2 snRNP, which plays a crucial role in pre-mRNA splicing. Hsh49p, comprising two RRMs, forms a heterodimer with Cus1p. We determined the crystal structures of Saccharomyces cerevisiae full-length Hsh49p as well as its RRM1 in complex with a minimal binding region of Cus1p (residues 290-368). The structures show that the Cus1 fragment binds to the α-helical surface of Hsh49p RRM1, opposite the four-stranded β-sheet, leaving the canonical RNA-binding surface available to bind RNA. Hsh49p binds the 5' end region of U2 snRNA via RRM1. Its affinity is increased in complex with Cus1(290-368)p, partly because an extended RNA-binding surface forms across the protein-protein interface. The Hsh49p RRM1-Cus1(290-368)p structure fits well into cryo-EM density of the B act spliceosome, corroborating the biological relevance of our crystal structure.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 101.98 kDa 
  • Atom Count: 5,799 
  • Modeled Residue Count: 712 
  • Deposited Residue Count: 897 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein HSH49A,
C,
E [auth F]
215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HSH49YOR319WO6142
UniProt
Find proteins for Q99181 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99181 
Go to UniProtKB:  Q99181
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99181
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cold sensitive U2 snRNA suppressor 1B,
D,
F [auth H]
84Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CUS1YMR240CYM9408.02C
UniProt
Find proteins for Q02554 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02554 
Go to UniProtKB:  Q02554
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02554
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.233 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.083α = 90
b = 142.083β = 90
c = 40.355γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description