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 
  • R-Value Observed: 0.183 

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
  • Primary Citation of Related Structures:  
    5I3L

  • 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, and others such as tandem PHD fingers of DPF3b ...

    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

    Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China. Electronic address: yanliliu@mail.ccnu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger protein DPF3A, B115Homo sapiensMutation(s): 0 
Gene Names: DPF3BAF45CCERD4
UniProt & NIH Common Fund Data Resources
Find proteins for Q92784 (Homo sapiens)
Explore Q92784 
Go to UniProtKB:  Q92784
PHAROS:  Q92784
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
H3K14ac peptideC21synthetic constructMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B], BA [auth B], D [auth A], E [auth A], F [auth A], G [auth A], Y [auth B], Z [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
EA [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
CA [auth B] , DA [auth B] , FA [auth B] , GA [auth B] , HA [auth B] , I [auth A] , IA [auth B] , J [auth A] , 
CA [auth B],  DA [auth B],  FA [auth B],  GA [auth B],  HA [auth B],  I [auth A],  IA [auth B],  J [auth A],  JA [auth B],  K [auth A],  KA [auth B],  L [auth A],  LA [auth B],  M [auth A],  MA [auth B],  N [auth A],  NA [auth B],  O [auth A],  OA [auth B],  P [auth A],  PA [auth B],  Q [auth A],  QA [auth B],  R [auth A],  RA [auth B],  S [auth A],  SA [auth B],  T [auth A],  U [auth A],  V [auth A],  W [auth A],  X [auth A]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
CL-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 
  • R-Value Observed: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.822α = 90
b = 121.641β = 90
c = 56.446γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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