5FUG

Crystal structure of a human YL1-H2A.Z-H2B complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular Basis and Specificity of H2A.Z-H2B Recognition and Deposition by the Histone Chaperone Yl1

Latrick, C.M.Marek, M.Ouararhni, K.Papin, C.Stoll, I.Ignatyeva, M.Obri, A.Ennifar, E.Dimitrov, S.Romier, C.Hamiche, A.

(2016) Nat.Struct.Mol.Biol. 23: 309

  • DOI: 10.1038/nsmb.3189

  • PubMed Abstract: 
  • H2A.Z, a widely conserved histone variant, is evicted from chromatin by the histone chaperone ANP32E. However, to date, no deposition chaperone for H2A.Z is known in metazoans. Here, we identify YL1 as a specific H2A.Z-deposition chaperone. The 2.7-Å ...

    H2A.Z, a widely conserved histone variant, is evicted from chromatin by the histone chaperone ANP32E. However, to date, no deposition chaperone for H2A.Z is known in metazoans. Here, we identify YL1 as a specific H2A.Z-deposition chaperone. The 2.7-Å-resolution crystal structure of the human YL1-H2A.Z-H2B complex shows that YL1 binding, similarly to ANP32E binding, triggers an extension of the H2A.Z αC helix. The interaction with YL1 is, however, more extensive and includes both the extended acidic patch and the entire DNA-binding surface of H2A.Z-H2B. Substitution of only four amino acid residues of H2A is sufficient for the formation of an H2A.Z-like interface specifically recognized by YL1. Collectively, our data reveal the molecular basis of H2A.Z-specific recognition by YL1 and shed light on the mechanism of H2A.Z transfer to the nucleosome by the ATP-dependent chromatin-remodeling complexes SRCAP and P400-TIP60.


    Organizational Affiliation

    Equipe Labélisée Ligue Contre le Cancer, Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTONE H2A.Z
A, D, G, J
110Homo sapiensMutation(s): 0 
Gene Names: H2AFZ (H2AZ)
Find proteins for P0C0S5 (Homo sapiens)
Go to Gene View: H2AFZ
Go to UniProtKB:  P0C0S5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HISTONE H2B TYPE 1-J
B, E, H, K
96Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ (H2BFR)
Find proteins for P06899 (Homo sapiens)
Go to Gene View: HIST1H2BJ
Go to UniProtKB:  P06899
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG
C, F, I, L
68Homo sapiensMutation(s): 0 
Gene Names: VPS72 (TCFL1, YL1)
Find proteins for Q15906 (Homo sapiens)
Go to Gene View: VPS72
Go to UniProtKB:  Q15906
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 36.120α = 90.00
b = 150.680β = 91.47
c = 92.610γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Database references
  • Version 1.2: 2016-03-23
    Type: Database references
  • Version 1.3: 2016-04-20
    Type: Database references