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- PDB-8cj3: Urea-based foldamer inhibitor c3u_7 chimera in complex with ASF1 ... -

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Basic information

Entry
Database: PDB / ID: 8cj3
TitleUrea-based foldamer inhibitor c3u_7 chimera in complex with ASF1 histone chaperone
Components
  • Histone chaperone ASF1A
  • c3u_7 chimera 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone chaperone ASF1A
B: c3u_7 chimera inhibitor of histone chaperone ASF1


Theoretical massNumber of molelcules
Total (without water)19,3082
Polymers19,3082
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, 1:1 complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-4 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.906, 133.906, 63.429
Angle α, β, γ (deg.)90, 90, 120
Int Tables number172
Space group name H-MP64

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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.: 1
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_7 chimera inhibitor of histone chaperone ASF1


Mass: 1379.699 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Sequence of a short peptide-oligourea chimera known to bind ASF1
Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 8.5 Å3/Da / Density % sol: 85.53 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium fluoride 20% (w/v) PEG 3350

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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: Jun 3, 2017
RadiationMonochromator: 0.97857 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3→46.047 Å / Num. obs: 10565 / % possible obs: 80.08 % / Redundancy: 20.42 % / CC1/2: 0.999 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.041 / Rrim(I) all: 0.184 / Net I/σ(I): 17.083
Reflection shellResolution: 3→3.078 Å / Redundancy: 21.88 % / Mean I/σ(I) obs: 1.132 / Num. unique obs: 238 / CC1/2: 0.5692 / Rpim(I) all: 0.661 / % possible all: 24.59

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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: 3→29.61 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.336 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.322 / SU Rfree Blow DPI: 0.243 / SU Rfree Cruickshank DPI: 0.251
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 545 -RANDOM
Rwork0.2027 ---
obs0.2034 10553 80.1 %-
Displacement parametersBiso mean: 74.51 Å2
Baniso -1Baniso -2Baniso -3
1-3.2985 Å20 Å20 Å2
2--3.2985 Å20 Å2
3----6.597 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 3→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1340 0 0 16 1356
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081374HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.921868HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d488SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes253HARMONIC5
X-RAY DIFFRACTIONt_it1374HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion172SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact928SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion15.76
LS refinement shellResolution: 3→3.13 Å
RfactorNum. reflection% reflection
Rfree0.387 28 -
Rwork0.3069 --
obs0.3122 391 25.59 %
Refinement TLS params.Origin x: 51.2968 Å / Origin y: -45.3674 Å / Origin z: -19.7781 Å
111213212223313233
T0.0241 Å2-0.0073 Å2-0.0457 Å2--0.1917 Å2-0.1358 Å2---0.2926 Å2
L9.7366 °22.026 °2-2.5568 °2-4.3047 °2-0.5187 °2--4.3055 °2
S0.1159 Å °0.0602 Å °0.124 Å °0.0602 Å °-0.2774 Å °-0.3604 Å °0.124 Å °-0.3604 Å °0.1614 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|* B|*}A1 - 154
2X-RAY DIFFRACTION1{A|* B|*}B0
3X-RAY DIFFRACTION1{A|* B|*}B1 - 2
4X-RAY DIFFRACTION1{A|* B|*}B3
5X-RAY DIFFRACTION1{A|* B|*}B4 - 6
6X-RAY DIFFRACTION1{A|* B|*}B7 - 10

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