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- PDB-8bv1: Peptide inhibitor P4 in complex with ASF1 histone chaperone -

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Basic information

Entry
Database: PDB / ID: 8bv1
TitlePeptide inhibitor P4 in complex with ASF1 histone chaperone
Components
  • Histone chaperone ASF1A
  • P4 peptide inhibitor of histone chaperone ASF1
KeywordsCHAPERONE / Inhibitor / ASF1 / Histone / protein-protein interaction
Function / homology
Function and homology information


histone chaperone activity / muscle cell differentiation / DNA replication-dependent chromatin assembly / DNA repair-dependent chromatin remodeling / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / osteoblast differentiation / nucleosome assembly / site of double-strand break / histone binding ...histone chaperone activity / muscle cell differentiation / DNA replication-dependent chromatin assembly / DNA repair-dependent chromatin remodeling / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / osteoblast differentiation / nucleosome assembly / site of double-strand break / histone binding / DNA repair / chromatin binding / chromatin / protein-containing complex / nucleoplasm / nucleus
Similarity search - Function
Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone
Similarity search - Domain/homology
Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.834 Å
AuthorsPerrin, M.E. / Li, B. / Mbianda, J. / Ropars, V. / Legrand, P. / Douat, C. / Ochsenbein, F. / Guichard, G.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE18-0038 France
Fondation ARCPGA1*20160203953 France
Agence Nationale de la Recherche (ANR)ANR-20-CE18-0038 France
CitationJournal: Chem.Commun.(Camb.) / Year: 2023
Title: Unexpected binding modes of inhibitors to the histone chaperone ASF1 revealed by a foldamer scanning approach.
Authors: Perrin, M.E. / Li, B. / Mbianda, J. / Bakail, M. / Andre, C. / Moal, G. / Legrand, P. / Ropars, V. / Douat, C. / Ochsenbein, F. / Guichard, G.
History
DepositionDec 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone chaperone ASF1A
B: Histone chaperone ASF1A
C: Histone chaperone ASF1A
D: Histone chaperone ASF1A
E: Histone chaperone ASF1A
F: Histone chaperone ASF1A
N: P4 peptide inhibitor of histone chaperone ASF1
G: P4 peptide inhibitor of histone chaperone ASF1
K: P4 peptide inhibitor of histone chaperone ASF1
H: P4 peptide inhibitor of histone chaperone ASF1
L: P4 peptide inhibitor of histone chaperone ASF1
I: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,40227
Polymers116,02012
Non-polymers1,38115
Water2,648147
1
A: Histone chaperone ASF1A
N: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8898
Polymers19,3372
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-13 kcal/mol
Surface area8700 Å2
MethodPISA
2
B: Histone chaperone ASF1A
K: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6135
Polymers19,3372
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-6 kcal/mol
Surface area8720 Å2
MethodPISA
3
C: Histone chaperone ASF1A
I: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4293
Polymers19,3372
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-5 kcal/mol
Surface area8370 Å2
MethodPISA
4
D: Histone chaperone ASF1A
L: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4293
Polymers19,3372
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-4 kcal/mol
Surface area8600 Å2
MethodPISA
5
E: Histone chaperone ASF1A
G: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6135
Polymers19,3372
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-6 kcal/mol
Surface area8730 Å2
MethodPISA
6
F: Histone chaperone ASF1A
H: P4 peptide inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4293
Polymers19,3372
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-6 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.885, 123.885, 179.308
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Histone chaperone ASF1A / Anti-silencing function protein 1 homolog A / hAsf1a / CCG1-interacting factor A / hCIA


Mass: 17927.998 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Histone chaperone that facilitates histone deposition and histone exchange and removal during nucleosome assembly and disassembly
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1A, CGI-98, HSPC146 / Plasmid: pETM30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9Y294
#2: Protein/peptide
P4 peptide inhibitor of histone chaperone ASF1


Mass: 1408.718 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: Sequence of a short alpha-helical peptide known to bind ASF1
Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5 30% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2022 / Details: KB Mirrors
RadiationMonochromator: 0.97857 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.834→49.372 Å / Num. obs: 56883 / % possible obs: 88.79 % / Redundancy: 14.27 % / CC1/2: 0.9979 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.043 / Rrim(I) all: 0.162 / Net I/σ(I): 13.13
Reflection shellResolution: 2.834→2.907 Å / Redundancy: 13.97 % / Mean I/σ(I) obs: 1.446 / Num. unique obs: 1058 / CC1/2: 0.6066 / Rpim(I) all: 0.635 / % possible all: 22.49

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
STARANISOdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6f0h

6f0h


Resolution: 2.834→29.79 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.355 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.332 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.248
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 2830 4.98 %RANDOM
Rwork0.2037 ---
obs0.2045 56834 88.8 %-
Displacement parametersBiso mean: 99.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.0137 Å20 Å20 Å2
2--0.0137 Å20 Å2
3----0.0273 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.834→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8045 0 90 147 8282
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088324HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9111335HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2850SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1511HARMONIC5
X-RAY DIFFRACTIONt_it8324HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1038SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5456SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion19.6
LS refinement shellResolution: 2.834→2.91 Å
RfactorNum. reflection% reflection
Rfree0.3283 53 -
Rwork0.3207 1084 -
obs--23.15 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8652-0.9998-2.89390.96280.63514.9189-0.0105-0.20920.0331-0.2092-0.053-0.14030.0331-0.14030.0634-0.2097-0.04320.0444-0.15380.0326-0.113-57.111634.2595-17.5294
22.77790.53930.94825.36751.44734.6809-0.0889-0.4488-0.332-0.44880.13810.2567-0.3320.2567-0.0492-0.09130.010.1768-0.25790.0482-0.09-21.347826.1306-40.295
33.3401-0.4125-1.17426.1384-1.26615.5977-0.26061.01440.37811.01440.10750.19350.37810.19350.15320.3464-0.00150.197-0.22640.098-0.0394-37.257166.4618-33.5468
44.59020.72570.20716.8837-0.19353.8933-0.0419-0.94160.622-0.94160.0537-0.52270.622-0.5227-0.01180.3169-0.0994-0.0894-0.1742-0.0279-0.1243-44.78424.6957-57.5592
56.4920.19162.24042.77270.82524.95130.2113-0.03940.5504-0.0394-0.0873-0.70490.5504-0.7049-0.124-0.2271-0.0484-0.00010.3172-0.0272-0.0396-16.176120.2012-6.255
66.65730.1285-0.27164.56381.75914.11380.140.0807-0.57970.08070.11250.7825-0.57970.7825-0.2526-0.1858-0.11990.04460.4981-0.3040.1798-15.448446.71015.1477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|* N|*}A1 - 155
2X-RAY DIFFRACTION1{A|* N|*}N0
3X-RAY DIFFRACTION1{A|* N|*}N1 - 2
4X-RAY DIFFRACTION1{A|* N|*}N3
5X-RAY DIFFRACTION1{A|* N|*}N4 - 10
6X-RAY DIFFRACTION1{A|* N|*}N11
7X-RAY DIFFRACTION2{B|* K|*}B2 - 156
8X-RAY DIFFRACTION2{B|* K|*}K0
9X-RAY DIFFRACTION2{B|* K|*}K1 - 2
10X-RAY DIFFRACTION2{B|* K|*}K3
11X-RAY DIFFRACTION2{B|* K|*}K4 - 10
12X-RAY DIFFRACTION2{B|* K|*}K11
13X-RAY DIFFRACTION3{C|* I|*}C2 - 153
14X-RAY DIFFRACTION3{C|* I|*}I0
15X-RAY DIFFRACTION3{C|* I|*}I1 - 2
16X-RAY DIFFRACTION3{C|* I|*}I3
17X-RAY DIFFRACTION3{C|* I|*}I4 - 10
18X-RAY DIFFRACTION3{C|* I|*}I11
19X-RAY DIFFRACTION4{D|* L|*}D2 - 155
20X-RAY DIFFRACTION4{D|* L|*}L0
21X-RAY DIFFRACTION4{D|* L|*}L1 - 2
22X-RAY DIFFRACTION4{D|* L|*}L3
23X-RAY DIFFRACTION4{D|* L|*}L4 - 10
24X-RAY DIFFRACTION4{D|* L|*}L11
25X-RAY DIFFRACTION5{E|* G|*}E2 - 155
26X-RAY DIFFRACTION5{E|* G|*}G0
27X-RAY DIFFRACTION5{E|* G|*}G1 - 2
28X-RAY DIFFRACTION5{E|* G|*}G3
29X-RAY DIFFRACTION5{E|* G|*}G4 - 10
30X-RAY DIFFRACTION5{E|* G|*}G11
31X-RAY DIFFRACTION6{F|* H|*}F2 - 155
32X-RAY DIFFRACTION6{F|* H|*}H0
33X-RAY DIFFRACTION6{F|* H|*}H1 - 2
34X-RAY DIFFRACTION6{F|* H|*}H3
35X-RAY DIFFRACTION6{F|* H|*}H4 - 10
36X-RAY DIFFRACTION6{F|* H|*}H11

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