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Yorodumi- PDB-5e5a: Crystal structure of the chromatin-tethering domain of Human cyto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e5a | ||||||||||||||||||||||||
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Title | Crystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein bound to the nucleosome core particle | ||||||||||||||||||||||||
Components |
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Keywords | PROTEIN BINDING/VIRAL PROTEIN/DNA / NCP / IE1 / hCMV / CTD / PROTEIN BINDING-VIRAL PROTEIN-DNA complex | ||||||||||||||||||||||||
Function / homology | Function and homology information : / DNA-templated viral transcription / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / structural constituent of chromatin / nucleosome / nucleosome assembly / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / protein heterodimerization activity / host cell nucleus / DNA binding ...: / DNA-templated viral transcription / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / structural constituent of chromatin / nucleosome / nucleosome assembly / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / protein heterodimerization activity / host cell nucleus / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) Human herpesvirus 5 strain Towne | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.809 Å | ||||||||||||||||||||||||
Authors | Fang, Q. / Chen, P. / Wang, M. / Fang, J. / Yang, N. / Li, G. / Xu, R.M. | ||||||||||||||||||||||||
Funding support | China, 7items
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Citation | Journal: Elife / Year: 2016 Title: Human cytomegalovirus IE1 protein alters the higher-order chromatin structure by targeting the acidic patch of the nucleosome Authors: Fang, Q. / Chen, P. / Wang, M. / Fang, J. / Yang, N. / Li, G. / Xu, R.M. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e5a.cif.gz | 332.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e5a.ent.gz | 252.1 KB | Display | PDB format |
PDBx/mmJSON format | 5e5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e5a_validation.pdf.gz | 509.5 KB | Display | wwPDB validaton report |
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Full document | 5e5a_full_validation.pdf.gz | 516.9 KB | Display | |
Data in XML | 5e5a_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 5e5a_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/5e5a ftp://data.pdbj.org/pub/pdb/validation_reports/e5/5e5a | HTTPS FTP |
-Related structure data
Related structure data | 1aoiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#2: Protein | Mass: 15435.126 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: P84233 #3: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: P62799 #4: Protein | Mass: 14109.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS #5: Protein | Mass: 13655.948 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: P02281 |
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-DNA chain / Protein/peptide , 2 types, 3 molecules IJK
#1: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a #6: Protein/peptide | | Mass: 1703.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 5 strain Towne / References: UniProt: Q6SWP6, UniProt: P03169*PLUS |
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-Non-polymers , 2 types, 234 molecules
#7: Chemical | ChemComp-MG / #8: Water | ChemComp-HOH / | |
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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: 2.64 Å3/Da / Density % sol: 58.41 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: sodium cacodylate, magnesium acetate, 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.0308 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0308 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→30 Å / Num. obs: 52496 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 53.33 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.056 / Rrim(I) all: 0.144 / Χ2: 1.022 / Net I/av σ(I): 12.5 / Net I/σ(I): 5 / Num. measured all: 346849 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID: 1AOI Resolution: 2.809→30 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 165.06 Å2 / Biso mean: 60.7308 Å2 / Biso min: 15.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.809→30 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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