5OV3 | pdb_00005ov3

Structure of the RbBP5 beta-propeller domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.271 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The structure of the RbBP5 beta-propeller domain reveals a surface with potential nucleic acid binding sites.

Mittal, A.Hobor, F.Zhang, Y.Martin, S.R.Gamblin, S.J.Ramos, A.Wilson, J.R.

(2018) Nucleic Acids Res 46: 3802-3812

  • DOI: https://doi.org/10.1093/nar/gky199
  • Primary Citation Related Structures: 
    5OV3

  • PubMed Abstract: 

    The multi-protein complex WRAD, formed by WDR5, RbBP5, Ash2L and Dpy30, binds to the MLL SET domain to stabilize the catalytically active conformation required for histone H3K4 methylation. In addition, the WRAD complex contributes to the targeting of the activated complex to specific sites on chromatin. RbBP5 is central to MLL catalytic activation, by making critical contacts with the other members of the complex. Interestingly its only major structural domain, a canonical WD40 repeat β-propeller, is not implicated in this function. Here, we present the structure of the RbBP5 β-propeller domain revealing a distinct, feature rich surface, dominated by clusters of Arginine residues. Our nuclear magnetic resonance binding data supports the hypothesis that in addition to the role of RbBP5 in catalytic activation, its β-propeller domain is a platform for the recruitment of the MLL complexes to chromatin targets through its direct interaction with nucleic acids.


  • Organizational Affiliation
    • The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.

Macromolecule Content 

  • Total Structure Weight: 85.99 kDa 
  • Atom Count: 5,153 
  • Modeled Residue Count: 653 
  • Deposited Residue Count: 768 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinoblastoma-binding protein 5
A, B
381Mus musculusMutation(s): 1 
Gene Names: Rbbp5
UniProt
Find proteins for Q8BX09 (Mus musculus)
Explore Q8BX09 
Go to UniProtKB:  Q8BX09
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BX09
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinoblastoma-binding protein 56Mus musculusMutation(s): 1 
Gene Names: Rbbp5
UniProt
Find proteins for Q8BX09 (Mus musculus)
Explore Q8BX09 
Go to UniProtKB:  Q8BX09
Entity Groups
UniProt GroupQ8BX09
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.271 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.809α = 90
b = 71.897β = 90
c = 178.269γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Francis Crick InstituteUnited KingdomFC001078

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description