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- PDB-6f0g: Crystal structure ASF1-ip3 -

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Basic information

Entry
Database: PDB / ID: 6f0g
TitleCrystal structure ASF1-ip3
Components
  • Histone chaperone ASF1A
  • ip3
KeywordsCHAPERONE / protein-peptide complexe
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 / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsGaubert, A. / Guichard, B. / Richet, N. / Le Du, M.H. / Andreani, J. / Guerois, R. / Ochsenbein, F.
Funding support France, 4items
OrganizationGrant numberCountry
French National Research AgencyBREAKABOUND France
French National Research AgencyCHAPINHIB France
French National Research AgencyFRISBI France
French National Research AgencyBIPBIP France
CitationJournal: Cell Chem Biol / Year: 2019
Title: Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.
Authors: Bakail, M. / Gaubert, A. / Andreani, J. / Moal, G. / Pinna, G. / Boyarchuk, E. / Gaillard, M.C. / Courbeyrette, R. / Mann, C. / Thuret, J.Y. / Guichard, B. / Murciano, B. / Richet, N. / ...Authors: Bakail, M. / Gaubert, A. / Andreani, J. / Moal, G. / Pinna, G. / Boyarchuk, E. / Gaillard, M.C. / Courbeyrette, R. / Mann, C. / Thuret, J.Y. / Guichard, B. / Murciano, B. / Richet, N. / Poitou, A. / Frederic, C. / Le Du, M.H. / Agez, M. / Roelants, C. / Gurard-Levin, Z.A. / Almouzni, G. / Cherradi, N. / Guerois, R. / Ochsenbein, F.
History
DepositionNov 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: ip3
D: ip3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6066
Polymers41,4144
Non-polymers1922
Water3,297183
1
A: Histone chaperone ASF1A
C: ip3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8033
Polymers20,7072
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-19 kcal/mol
Surface area9450 Å2
MethodPISA
2
B: Histone chaperone ASF1A
D: ip3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8033
Polymers20,7072
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-20 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.470, 73.470, 343.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-356-

HOH

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1A, CGI-98, HSPC146 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q9Y294
#2: Protein/peptide ip3


Mass: 2779.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: rational design / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Citrate 0.1M pH 2.5, LiSO4 0.25M, PEG8000 7%

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. obs: 16434 / % possible obs: 99.6 % / Redundancy: 7.9 % / Biso Wilson estimate: 28.48 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.1299 / % possible all: 97.5

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
BUSTERphasing
RefinementResolution: 2.3→38.88 Å / Cor.coef. Fo:Fc: 0.9074 / Cor.coef. Fo:Fc free: 0.8756 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 1009 5.39 %RANDOM
Rwork0.2099 ---
obs0.2129 16434 99.6 %-
Displacement parametersBiso mean: 38.03 Å2
Baniso -1Baniso -2Baniso -3
1-3.8208 Å20 Å20 Å2
2--3.8208 Å20 Å2
3----7.6416 Å2
Refine analyzeLuzzati coordinate error obs: 0.303 Å
Refinement stepCycle: 1 / Resolution: 2.3→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 10 183 3045
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012930HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.163994HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d984SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes418HARMONIC5
X-RAY DIFFRACTIONt_it2930HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion21.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion372SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3361SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.33 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2734 183 6.24 %
Rwork0.2274 2752 -
all0.2304 2935 -
Refinement TLS params.

Method: refined / 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)
12.50980.2629-0.47851.36510.27820.6816-0.09510.3812-0.0659-0.15450.013-0.0047-0.0434-0.05670.0821-0.15970.00010.0069-0.118-0.0070.078820.989519.002627.296
22.19880.16040.11521.6987-0.30421.0512-0.07160.25010.0517-0.10350.03310.02550.01860.0070.0385-0.15380.0002-0.0068-0.1444-0.00720.08515.737744.661227.2591
33.5749-0.0565-1.35113.1381-0.13232.7817-0.14870.2098-0.26170.29850.1439-0.04020.2160.04040.0048-0.28990.0263-0.0193-0.1883-0.03040.30414.24037.461931.5794
44.76870.47892.1764.8928-2.08134.1477-0.05610.14830.03860.14420.058-0.125-0.3578-0.0665-0.0019-0.22670.00870.0258-0.25740.01220.30222.52156.232331.6525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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