2XU7 | pdb_00002xu7

Structural basis for RbAp48 binding to FOG-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.225 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2XU7

This is version 1.3 of the entry. See complete history

Literature

Insights Into Association of the Nurd Complex with Fog-1 from the Crystal Structure of an Rbap48-Fog- 1 Complex.

Lejon, S.Thong, S.Y.Murthy, A.Alqarni, S.Murzina, N.V.Blobel, G.A.Laue, E.D.Mackay, J.P.

(2011) J Biological Chem 286: 1196

  • DOI: https://doi.org/10.1074/jbc.M110.195842
  • Primary Citation Related Structures: 
    2XU7

  • PubMed Abstract: 

    Chromatin-modifying complexes such as the NuRD complex are recruited to particular genomic sites by gene-specific nuclear factors. Overall, however, little is known about the molecular basis for these interactions. Here, we present the 1.9 Å resolution crystal structure of the NuRD subunit RbAp48 bound to the 15 N-terminal amino acids of the GATA-1 cofactor FOG-1. The FOG-1 peptide contacts a negatively charged binding pocket on top of the RbAp48 β-propeller that is distinct from the binding surface used by RpAp48 to contact histone H4. We further show that RbAp48 interacts with the NuRD subunit MTA-1 via a surface that is distinct from its FOG-binding pocket, providing a first glimpse into the way in which NuRD assembly facilitates interactions with cofactors. Our RbAp48·FOG-1 structure provides insight into the molecular determinants of FOG-1-dependent association with the NuRD complex and into the links between transcription regulation and nucleosome remodeling.


  • Organizational Affiliation
    • Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 99.56 kDa 
  • Atom Count: 6,172 
  • Modeled Residue Count: 752 
  • Deposited Residue Count: 880 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HISTONE-BINDING PROTEIN RBBP4
A, B
425Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q09028 (Homo sapiens)
Explore Q09028 
Go to UniProtKB:  Q09028
PHAROS:  Q09028
GTEx:  ENSG00000162521 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09028
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ZINC FINGER PROTEIN ZFPM1
C, D
15Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IX07 (Homo sapiens)
Explore Q8IX07 
Go to UniProtKB:  Q8IX07
PHAROS:  Q8IX07
GTEx:  ENSG00000179588 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IX07
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.225 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.745α = 90
b = 59.843β = 93.55
c = 100.648γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description