8BV1 | pdb_00008bv1

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 (Depositor), 0.212 (DCC)
R-Value Work:
0.204 (Depositor), 0.193 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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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 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
Modeled Residue Count: 1,002
Deposited Residue Count: 1,026
Unique protein chains: 2

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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 Z [auth E] SDF format, chain Y [auth E] SDF format, chain X [auth E] SDF format, chain W [auth D] SDF format, chain V [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain AA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain W [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain W [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain AA [auth F]	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 (Depositor), 0.212 (DCC)
R-Value Work: 0.204 (Depositor), 0.193 (DCC)
R-Value Observed: 0.204 (Depositor)

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

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View more in-depth experimental data

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