6AE8

Structure insight into histone chaperone Chz1-mediated H2A.Z recognition and replacement


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Literature

Structural insights into histone chaperone Chz1-mediated H2A.Z recognition and histone replacement.

Wang, Y.Liu, S.Sun, L.Xu, N.Shan, S.Wu, F.Liang, X.Huang, Y.Luk, E.Wu, C.Zhou, Z.

(2019) PLoS Biol 17: e3000277-e3000277

  • DOI: 10.1371/journal.pbio.3000277
  • Primary Citation of Related Structures:  
    6AE8

  • PubMed Abstract: 
  • Chz1 is a specific chaperone for the histone variant H2A.Z in budding yeast. The ternary complex formed by Chz1 and H2A.Z-H2B dimer is the major in vivo substrate of Swi2/snif2-related 1 (SWR1), the ATP-dependent chromatin remodeling enzyme that deposits H2A ...

    Chz1 is a specific chaperone for the histone variant H2A.Z in budding yeast. The ternary complex formed by Chz1 and H2A.Z-H2B dimer is the major in vivo substrate of Swi2/snif2-related 1 (SWR1), the ATP-dependent chromatin remodeling enzyme that deposits H2A.Z into chromatin. However, the structural basis for the binding preference of Chz1 for H2A.Z over H2A and the mechanism by which Chz1 modulates the histone replacement remain elusive. Here, we show that Chz1 utilizes 2 distinct structural domains to engage the H2A.Z-H2B dimer for optimal and specific recognition of H2A.Z. The middle region of Chz1 (Chz1-M) directly interacts with 2 highly conserved H2A.Z-specific residues (Gly98 and Ala57) and dictates a modest preference for H2A.Z-H2B. In addition, structural and biochemical analysis show that the C-terminal region of Chz1 (Chz1-C) harbors a conserved DEF/Y motif, which reflects the consecutive D/E residues followed by a single aromatic residue, to engage an arginine finger and a hydrophobic pocket in H2A.Z-H2B, enhancing the binding preference for H2A.Z-H2B. Furthermore, Chz1 facilitates SWR1-mediated H2A.Z deposition by alleviating inhibition caused by aggregation of excess free histones, providing insights into how Chz1 controls the bioavailability of H2A.Z to assist SWR1 in promoter-specific installation of a histone mark. Our study elucidates a novel H2A.Z-recognition mechanism and uncovers a molecular rationale for binding of free histone by specialized histone chaperones in vivo.


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B.1,Histone H2A.ZA, C [auth B]193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTZ1
UniProt
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02293 
Go to UniProtKB:  P02293
Find proteins for Q12692 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12692 
Go to UniProtKB:  Q12692
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A.Z-specific chaperone CHZ1B [auth C], D120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CHZ1YER030W
UniProt
Find proteins for P40019 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40019 
Go to UniProtKB:  P40019
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCN (Subject of Investigation/LOI)
Query on BCN

Download Ideal Coordinates CCD File 
E [auth A], F [auth B]BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.082α = 72.37
b = 46.21β = 70.92
c = 56.662γ = 70.6
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2015CB856200
Ministry of Science and Technology (China)China31521002

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Advisory, Data collection, Database references, Derived calculations