8BV1

Peptide inhibitor P4 in complex with ASF1 histone chaperone

PDB DOI: https://doi.org/10.2210/pdb8BV1/pdb

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

Deposited: 2022-12-01 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: 2.83 Å
R-Value Free: 0.221
R-Value Work: 0.204
R-Value Observed: 0.204

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 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: 117.4 kDa
Atom Count: 8,282
Modelled Residue Count: 1,002
Deposited Residue Count: 1,026
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, E A, B, C, D, E, F	158	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
P4 peptide inhibitor of histone chaperone ASF1	G [auth N] H [auth G] I [auth K] J [auth H] K [auth L] G [auth N], H [auth G], I [auth K], J [auth H], K [auth L], L [auth I]	13	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth C] SDF format, chain W [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E]	AA [auth F] M [auth A] N [auth A] O [auth A] P [auth A] AA [auth F], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth B], T [auth B], U [auth B], V [auth C], W [auth D], X [auth E], Y [auth E], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALN Query on ALN	G [auth N] H [auth G] I [auth K] J [auth H] K [auth L] G [auth N], H [auth G], I [auth K], J [auth H], K [auth L], L [auth I]	L-PEPTIDE LINKING	C₁₃ H₁₃ N O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free: 0.221
R-Value Work: 0.204
R-Value Observed: 0.204
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.885	α = 90
b = 123.885	β = 90
c = 179.308	γ = 90

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