5FUG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1038/nsmb.3189
  • Primary Citation of Related Structures:  
    5FUG

  • 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-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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HISTONE H2A.Z
A, D, G, J
110Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S5 (Homo sapiens)
Explore P0C0S5 
Go to UniProtKB:  P0C0S5
PHAROS:  P0C0S5
GTEx:  ENSG00000164032 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0S5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HISTONE H2B TYPE 1-J
B, E, H, K
96Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
PHAROS:  P06899
GTEx:  ENSG00000124635 
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UniProt GroupP06899
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG
C, F, I, L
68Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15906 (Homo sapiens)
Explore Q15906 
Go to UniProtKB:  Q15906
PHAROS:  Q15906
GTEx:  ENSG00000163159 
Entity Groups  
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UniProt GroupQ15906
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.12α = 90
b = 150.68β = 91.47
c = 92.61γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2016-03-23
    Changes: Database references
  • Version 1.3: 2016-04-20
    Changes: Database references
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description