4QC1

Crystal structure of human BAZ2B bromodomain in complex with an acetylated histone 3 peptide (H3K14ac)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis of histone tail recognition by human TIP5 PHD finger and bromodomain of the chromatin remodeling complex NoRC.

Tallant, C.Valentini, E.Fedorov, O.Overvoorde, L.Ferguson, F.M.Filippakopoulos, P.Svergun, D.I.Knapp, S.Ciulli, A.

(2015) Structure 23: 80-92

  • DOI: 10.1016/j.str.2014.10.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Binding of the chromatin remodeling complex NoRC to RNA complementary to the rDNA promoter mediates transcriptional repression. TIP5, the largest subunit of NoRC, is involved in recruitment to rDNA by interactions with promoter-bound TTF-I, pRNA, and ...

    Binding of the chromatin remodeling complex NoRC to RNA complementary to the rDNA promoter mediates transcriptional repression. TIP5, the largest subunit of NoRC, is involved in recruitment to rDNA by interactions with promoter-bound TTF-I, pRNA, and acetylation of H4K16. TIP5 domains that recognize posttranslational modifications on histones are essential for recruitment of NoRC to chromatin, but how these reader modules recognize site-specific histone tails has remained elusive. Here, we report crystal structures of PHD zinc finger and bromodomains from human TIP5 and BAZ2B in free form and bound to H3 and/or H4 histones. PHD finger functions as an independent structural module in recognizing unmodified H3 histone tails, and the bromodomain prefers H3 and H4 acetylation marks followed by a key basic residue, KacXXR. Further low-resolution analyses of PHD-bromodomain modules provide molecular insights into their trans histone tail recognition, required for nucleosome recruitment and transcriptional repression of the NoRC complex.


    Organizational Affiliation

    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK.,Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK.,Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK.,Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.,European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany.,Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK. Electronic address: a.ciulli@dundee.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain adjacent to zinc finger domain protein 2B
A, B
107Homo sapiensMutation(s): 0 
Gene Names: BAZ2B (KIAA1476)
Find proteins for Q9UIF8 (Homo sapiens)
Go to Gene View: BAZ2B
Go to UniProtKB:  Q9UIF8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
acetylated histone 3 peptide (H3K14ac)
D, E
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
D, E
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 29.724α = 90.00
b = 67.012β = 90.00
c = 136.055γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
REFMACrefinement
ADSCdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references