8CJ2

Urea-based foldamer inhibitor c3u_5 chimera in complex with ASF1 histone chaperone

PDB DOI: https://doi.org/10.2210/pdb8CJ2/pdb

Classification: CHAPERONE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-02-11 Released: 2023-07-05
Deposition Author(s): Perrin, M.E., Li, B., Mbianda, J., Ropars, V., Legrand, P., Douat, C., Ochsenbein, F., Guichard, G.
Funding Organization(s): Agence Nationale de la Recherche (ANR), Fondation ARC

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.215
R-Value Work: 0.193
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Unexpected binding modes of inhibitors to the histone chaperone ASF1 revealed by a foldamer scanning approach.

Perrin, M.E., Li, B., Mbianda, J., Bakail, M., Andre, C., Moal, G., Legrand, P., Ropars, V., Douat, C., Ochsenbein, F., Guichard, G.

(2023) Chem Commun (Camb) 59: 8696-8699

PubMed: 37347155 Search on PubMed
DOI: https://doi.org/10.1039/d3cc01891a
Primary Citation of Related Structures:
8BV1, 8CJ1, 8CJ2, 8CJ3

PubMed Abstract:
In the search for foldamer inhibitors of the histone chaperone ASF1, we explored the possibility of substituting four α-residues (≈one helix turn) by 3-urea segments and scanned the sequence of a short α-helical peptide known to bind ASF1. By analysing the impact of the different foldamer replacements within the peptide chain, we uncovered new binding modes of the peptide-urea chimeras to ASF1.

Organizational Affiliation

Joliot Institute, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), CEA Saclay, 91191 Gif-sur-Yvette, France. francoise.ochsenbein@cea.fr.

Macromolecule Content

Total Structure Weight: 78.11 kDa
Atom Count: 5,777
Modelled Residue Count: 657
Deposited Residue Count: 668
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone chaperone ASF1A	A, B, C, D	156	Homo sapiens	Mutation(s): 0 Gene Names: ASF1A, CGI-98, HSPC146
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y294
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
c3u_5 chimera inhibitor of histone chaperone ASF1	E, F, G, H	11	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain W [auth G] MOL2 format, chain W [auth G]	W [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain W [auth G] Interactions & Density Focus chain W [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth E] SDF format, chain U [auth F] SDF format, chain V [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F]	I [auth A] J [auth A] K [auth A] L [auth B] M [auth B] I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth C], Q [auth D], R [auth D], S [auth D], T [auth E], U [auth F], V [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALN Query on ALN	E, F, G, H	L-PEPTIDE LINKING	C₁₃ H₁₃ N O₂		ALA
QQ8 Query on QQ8	E, F, G, H	L-PEPTIDE LINKING	C₆ H₁₃ N₃ O₂		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.215
R-Value Work: 0.193
R-Value Observed: 0.194
Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.67	α = 90
b = 98.67	β = 90
c = 168.56	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
MxCuBE	data collection
XDS	data reduction
XDS	data scaling
STARANISO	data scaling
Coot	model building
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-20-CE18-0038
Fondation ARC	France	PGA1*20160203953
Agence Nationale de la Recherche (ANR)	France	ANR-20-CE18-0038

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2023-07-19
Changes: Database references
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations