6F0H | pdb_00006f0h

Crystal structure ASF1-ip4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.242 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6F0H

This is version 1.2 of the entry. See complete history

Literature

Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.

Bakail, M.Gaubert, A.Andreani, J.Moal, G.Pinna, G.Boyarchuk, E.Gaillard, M.C.Courbeyrette, R.Mann, C.Thuret, J.Y.Guichard, B.Murciano, B.Richet, N.Poitou, A.Frederic, C.Le Du, M.H.Agez, M.Roelants, C.Gurard-Levin, Z.A.Almouzni, G.Cherradi, N.Guerois, R.Ochsenbein, F.

(2019) Cell Chem Biol 26: 1573-1585.e10

  • DOI: https://doi.org/10.1016/j.chembiol.2019.09.002
  • Primary Citation Related Structures: 
    6F0F, 6F0G, 6F0H

  • PubMed Abstract: 

    Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.


  • Organizational Affiliation
    • Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), 91191 Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.

Macromolecule Content 

  • Total Structure Weight: 42 kDa 
  • Atom Count: 3,241 
  • Modeled Residue Count: 356 
  • Deposited Residue Count: 368 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone chaperone ASF1A
A, C
158Homo sapiensMutation(s): 0 
Gene Names: ASF1ACGI-98HSPC146
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y294 (Homo sapiens)
Explore Q9Y294 
Go to UniProtKB:  Q9Y294
PHAROS:  Q9Y294
GTEx:  ENSG00000111875 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y294
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ip4
B, D
26Homo sapiensMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT

Query on CIT



Download:Ideal Coordinates CCD File
J [auth C]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
H [auth B],
K [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
I [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.242 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.44α = 90
b = 73.44β = 90
c = 229.02γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceCHAPINHIB
French National Research AgencyFranceFRISBI
French National Research AgencyFranceBIPBIP

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description