5I3L

DPF3b in complex with H3K14ac peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of DPF3b in complex with an acetylated histone peptide.

Li, W.Zhao, A.Tempel, W.Loppnau, P.Liu, Y.

(2016) J.Struct.Biol. 195: 365-372

  • DOI: 10.1016/j.jsb.2016.07.001

  • PubMed Abstract: 
  • Histone acetylation plays an important role in chromatin dynamics and is associated with active gene transcription. This modification is written by acetyltransferases, erased by histone deacetylases and read out by bromodomain containing proteins, an ...

    Histone acetylation plays an important role in chromatin dynamics and is associated with active gene transcription. This modification is written by acetyltransferases, erased by histone deacetylases and read out by bromodomain containing proteins, and others such as tandem PHD fingers of DPF3b. Here we report the high resolution crystal structure of the tandem PHD fingers of DPF3b in complex with an H3K14ac peptide. In the complex structure, the histone peptide adopts an α-helical conformation, unlike previously observed by NMR, but similar to a previously reported MOZ-H3K14ac complex structure. Our crystal structure adds to existing evidence that points to the α-helix as a natural conformation of histone tails as they interact with histone-associated proteins.


    Organizational Affiliation

    Key Laboratory of Pesticide & Chemical Biology, College of Chemistry, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zinc finger protein DPF3
A, B
115Homo sapiensMutation(s): 0 
Gene Names: DPF3 (BAF45C, CERD4)
Find proteins for Q92784 (Homo sapiens)
Go to Gene View: DPF3
Go to UniProtKB:  Q92784
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
H3K14ac peptide
C
21Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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Download CCD File 
A, B
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
C
NON-POLYMERH2 N

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ALY
Query on ALY
C
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 99.822α = 90.00
b = 121.641β = 90.00
c = 56.446γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-08-03
    Type: Database references
  • Version 1.2: 2016-08-24
    Type: Database references
  • Version 1.3: 2017-08-09
    Type: Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2018-08-15
    Type: Data collection, Database references