5Y1Z

Crystal structure of ZMYND8 PHD-BROMO-PWWP tandem in complex with Drebrin ADF-H domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

Starting Models: experimental
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This is version 1.2 of the entry. See complete history


Literature

The Structure of the ZMYND8/Drebrin Complex Suggests a Cytoplasmic Sequestering Mechanism of ZMYND8 by Drebrin

Yao, N.Li, J.Liu, H.Wan, J.Liu, W.Zhang, M.

(2017) Structure 25: 1657-1666.e3

  • DOI: https://doi.org/10.1016/j.str.2017.08.014
  • Primary Citation of Related Structures:  
    5Y1Z

  • PubMed Abstract: 

    Malfunctions of the actin binding protein Drebrin have been implicated in various human diseases such as Alzheimer's disease, cognitive impairments, cancer, and digestive disorders, though with poorly understood mechanisms. The ADF-H domain of Drebrin does not contain actin binding and depolymerizing activity. Instead, it binds to a histone marker reader, ZMYND8. Here we present the high-resolution crystal structure of Drebrin ADF-H in complex with the ZMYND8 PHD-BROMO-PWWP tandem, elucidating the mechanistic basis governing the highly specific interaction of the two proteins. The structure reveals that the ZMYND8 PHD-BROMO-PWWP tandem forms a structural supramodule that is necessary for binding to Drebrin ADF-H. Drebrin ADF-H competes with modified histone for binding to ZMYND8. Binding of Drebrin can shuttle ZMYND8 from nucleus to cytoplasm in living cells. Taken together, our study uncovers a non-actin target binding mode for ADF-H domains, and suggests that Drebrin may regulate activities of epigenetic reader ZMYND8 via its cytoplasmic sequestration.


  • Organizational Affiliation

    Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Drebrin
A, B
137Homo sapiensMutation(s): 0 
Gene Names: DBN1D0S117E
UniProt & NIH Common Fund Data Resources
Find proteins for Q16643 (Homo sapiens)
Explore Q16643 
Go to UniProtKB:  Q16643
PHAROS:  Q16643
GTEx:  ENSG00000113758 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16643
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein kinase C-binding protein 1
C, D
324Homo sapiensMutation(s): 0 
Gene Names: ZMYND8KIAA1125PRKCBP1RACK7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULU4 (Homo sapiens)
Explore Q9ULU4 
Go to UniProtKB:  Q9ULU4
PHAROS:  Q9ULU4
GTEx:  ENSG00000101040 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULU4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
I [auth C]
J [auth C]
K [auth C]
O [auth D]
E [auth A],
I [auth C],
J [auth C],
K [auth C],
O [auth D],
P [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
Q [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth C]
G [auth C]
H [auth C]
L [auth D]
M [auth D]
F [auth C],
G [auth C],
H [auth C],
L [auth D],
M [auth D],
N [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.183α = 90
b = 138.095β = 90
c = 161.164γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description