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- PDB-8cj2: Urea-based foldamer inhibitor c3u_5 chimera in complex with ASF1 ... -

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Basic information

Entry
Database: PDB / ID: 8cj2
TitleUrea-based foldamer inhibitor c3u_5 chimera in complex with ASF1 histone chaperone
Components
  • Histone chaperone ASF1A
  • c3u_5 chimera inhibitor of histone chaperone ASF1
KeywordsCHAPERONE / Inhibitor / ASF1 / Histone / protein-protein interaction
Function / homology
Function and homology information


histone chaperone activity / DNA replication-dependent chromatin assembly / muscle cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / replication fork processing / osteoblast differentiation / nucleosome assembly / site of double-strand break / histone binding ...histone chaperone activity / DNA replication-dependent chromatin assembly / muscle cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.127 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
DepositionFeb 11, 2023Deposition 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone chaperone ASF1A
B: Histone chaperone ASF1A
C: Histone chaperone ASF1A
D: Histone chaperone ASF1A
E: c3u_5 chimera inhibitor of histone chaperone ASF1
F: c3u_5 chimera inhibitor of histone chaperone ASF1
G: c3u_5 chimera inhibitor of histone chaperone ASF1
H: c3u_5 chimera inhibitor of histone chaperone ASF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,17223
Polymers76,7868
Non-polymers1,38515
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, 1:2 complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12130 Å2
ΔGint-42 kcal/mol
Surface area31390 Å2
Unit cell
Length a, b, c (Å)98.67, 98.67, 168.56
Angle α, β, γ (deg.)90, 90, 120
Int Tables number171
Space group name H-MP62

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Components

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


Mass: 17799.869 Da / Num. of mol.: 4
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
c3u_5 chimera inhibitor of histone chaperone ASF1


Mass: 1396.706 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Sequence of a short peptide-oligourea chimera known to bind ASF1
Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.17 M ammonium sulfate 0.085 M NaOAc pH 4.6 25.5% PEG 2000 MME 15% (v/v) glycerol

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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: Jul 1, 2021 / Details: KB mirros
RadiationMonochromator: 0.97857 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.127→49.335 Å / Num. obs: 51901 / % possible obs: 99.76 % / Redundancy: 21.23 % / CC1/2: 0.9993 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.024 / Rrim(I) all: 0.109 / Net I/σ(I): 20.119
Reflection shellResolution: 2.127→2.182 Å / Redundancy: 18.79 % / Rmerge(I) obs: 1.545 / Mean I/σ(I) obs: 2.007 / Num. unique obs: 3706 / CC1/2: 0.7649 / Rpim(I) all: 0.362 / % possible all: 96.79

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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 / Resolution: 2.127→24.41 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.184 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.153
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2593 5 %RANDOM
Rwork0.1933 ---
obs0.1944 51870 99.7 %-
Displacement parametersBiso mean: 57.15 Å2
Baniso -1Baniso -2Baniso -3
1--5.0323 Å20 Å20 Å2
2---5.0323 Å20 Å2
3---10.0646 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.127→24.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5339 0 89 349 5777
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085549HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.927541HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1979SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1004HARMONIC5
X-RAY DIFFRACTIONt_it5549HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion686SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4193SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion20.57
LS refinement shellResolution: 2.13→2.14 Å
RfactorNum. reflection% reflection
Rfree0.3164 51 4.91 %
Rwork0.2988 1038 -
obs--88.24 %
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)
11.56760.0030.58090.8866-0.14192.82890.05070.14610.13040.1461-0.0214-0.17620.1304-0.1762-0.02930.0755-0.0894-0.0354-0.11490.0417-0.1045-36.4438-20.619820.5012
21.173-0.48610.24152.0594-0.08622.6123-0.058-0.29030.0287-0.29030.1281-0.10290.0287-0.1029-0.07020.0341-0.08660.0074-0.11070.0433-0.0972-46.3887-43.170833.2506
33.85930.6967-0.74423.01050.3394.41480.15650.54-0.26970.54-0.28130.0691-0.26970.06910.12480.1104-0.1487-0.1779-0.13170.09470.0154-18.7741-2.199716.9345
41.8441-0.0486-0.12163.05060.60653.6526-0.1523-0.5164-0.232-0.51640.1890.2567-0.2320.2567-0.03680.1753-0.15520.0394-0.1125-0.0070.10563.5028-17.872129.9202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|* E|*}
2X-RAY DIFFRACTION2{B|* F|*}
3X-RAY DIFFRACTION3{C|* G|*}
4X-RAY DIFFRACTION4{D|* H|*}

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