+Open data
-Basic information
Entry | Database: PDB / ID: 8bv1 | ||||||||||||
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Title | Peptide inhibitor P4 in complex with ASF1 histone chaperone | ||||||||||||
Components |
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Keywords | CHAPERONE / 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 | ||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.834 Å | ||||||||||||
Authors | Perrin, M.E. / Li, B. / Mbianda, J. / Ropars, V. / Legrand, P. / Douat, C. / Ochsenbein, F. / Guichard, G. | ||||||||||||
Funding support | France, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bv1.cif.gz | 418 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bv1.ent.gz | 351.4 KB | Display | PDB format |
PDBx/mmJSON format | 8bv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bv1_validation.pdf.gz | 507.7 KB | Display | wwPDB validaton report |
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Full document | 8bv1_full_validation.pdf.gz | 513.5 KB | Display | |
Data in XML | 8bv1_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 8bv1_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/8bv1 ftp://data.pdbj.org/pub/pdb/validation_reports/bv/8bv1 | HTTPS FTP |
-Related structure data
Related structure data | 8cj1C 8cj2C 8cj3C 6f0hS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | 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 | 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 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.1 % |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5 30% (w/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2022 / Details: KB Mirrors |
Radiation | Monochromator: 0.97857 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Displacement parameters | Biso mean: 99.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.38 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.834→29.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.834→2.91 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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