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- PDB-8cj1: Urea-based foldamer inhibitor c3u_3 chimera in complex with ASF1 ... -

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Basic information

Entry
Database: PDB / ID: 8cj1
TitleUrea-based foldamer inhibitor c3u_3 chimera in complex with ASF1 histone chaperone
Components
  • Histone chaperone ASF1A
  • c3u_3 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: 2.564 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
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane
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

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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: Histone chaperone ASF1A
F: Histone chaperone ASF1A
G: Histone chaperone ASF1A
H: Histone chaperone ASF1A
I: c3u_3 chimera inhibitor of histone chaperone ASF1
J: c3u_3 chimera inhibitor of histone chaperone ASF1
K: c3u_3 chimera inhibitor of histone chaperone ASF1
L: c3u_3 chimera inhibitor of histone chaperone ASF1


Theoretical massNumber of molelcules
Total (without water)146,34012
Polymers146,34012
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, 1:1 complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.564, 93.225, 227.684
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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.: 8
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_3 chimera inhibitor of histone chaperone ASF1


Mass: 728.930 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 40% (w/v) PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2017 / 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: 2.564→86.273 Å / Num. obs: 36613 / % possible obs: 57.79 % / Redundancy: 13.31 % / CC1/2: 0.9903 / Rpim(I) all: 0.112 / Rrim(I) all: 0.413 / Net I/σ(I): 6.844
Reflection shellResolution: 2.564→2.63 Å / Redundancy: 4.09 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 117 / CC1/2: 0.3218 / Rpim(I) all: 0.485 / % possible all: 2.54

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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: 2.564→27.88 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.842 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.449
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 1835 4.98 %RANDOM
Rwork0.2251 ---
obs0.2279 36613 55.7 %-
Displacement parametersBiso mean: 47.33 Å2
Baniso -1Baniso -2Baniso -3
1--3.2106 Å20 Å20 Å2
2--0.1454 Å20 Å2
3---3.0651 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.564→27.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10094 0 0 301 10395
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00810354HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.914149HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3470SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1790HARMONIC5
X-RAY DIFFRACTIONt_it10354HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1325SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6950SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion17.98
LS refinement shellResolution: 2.564→2.72 Å
RfactorNum. reflection% reflection
Rfree0.3769 23 3.12 %
Rwork0.2836 --
obs--5.58 %
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)
11.8997-0.42440.25483.5867-1.34696.2085-0.08110.0654-0.46130.06540.0045-0.0085-0.4613-0.00850.0766-0.268-0.0462-0.019-0.2175-0.0398-0.1527-8.81114.772855.9338
23.73910.1476-2.14862.20710.15728.49290.08890.0725-0.17620.0725-0.0336-0.5903-0.1762-0.5903-0.0553-0.2754-0.0131-0.0358-0.19790.0203-0.19119.045532.24881.1535
32.7568-0.3814-0.18785.01722.482811.8479-0.11230.39330.03550.39330.107-0.68690.0355-0.68690.0053-0.24630.0587-0.04330.04520.1165-0.0733-34.76310.085743.1255
43.6428-0.5230.31463.7647-1.944712.4637-0.06740.3412-0.21320.34120.00820.8438-0.21320.84380.0592-0.2075-0.03120.06970.119-0.1839-0.068636.117841.047737.9213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{B|* I|*}B1 - 154
2X-RAY DIFFRACTION1{B|* I|*}I6 - 9
3X-RAY DIFFRACTION1{B|* I|*}I10
4X-RAY DIFFRACTION2{C|* J|*}C1 - 154
5X-RAY DIFFRACTION2{C|* J|*}J6 - 9
6X-RAY DIFFRACTION2{C|* J|*}J10
7X-RAY DIFFRACTION3{E|* K|*}E1 - 154
8X-RAY DIFFRACTION3{E|* K|*}K5
9X-RAY DIFFRACTION3{E|* K|*}K6 - 9
10X-RAY DIFFRACTION3{E|* K|*}K10
11X-RAY DIFFRACTION4{G|* L|*}G1 - 154
12X-RAY DIFFRACTION4{G|* L|*}L6 - 9
13X-RAY DIFFRACTION4{G|* L|*}L10

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