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Yorodumi- PDB-6o5w: Crystal structure of MORC3 CW domain fused with viral influenza A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o5w | ||||||
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Title | Crystal structure of MORC3 CW domain fused with viral influenza A NS1 peptide | ||||||
Components | NS1-linked peptide,MORC family CW-type zinc finger protein 3 | ||||||
Keywords | TRANSCRIPTION / MORC3 / ATPase / NS1 / virus / histone / CW / chromatin | ||||||
Function / homology | Function and homology information negative regulation of interferon-beta production / maintenance of protein location in nucleus / negative regulation of fibroblast proliferation / antiviral innate immune response / methylated histone binding / post-embryonic development / PML body / nuclear matrix / positive regulation of cellular senescence / peptidyl-serine phosphorylation ...negative regulation of interferon-beta production / maintenance of protein location in nucleus / negative regulation of fibroblast proliferation / antiviral innate immune response / methylated histone binding / post-embryonic development / PML body / nuclear matrix / positive regulation of cellular senescence / peptidyl-serine phosphorylation / protein-macromolecule adaptor activity / protein stabilization / protein phosphorylation / chromatin / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.412 Å | ||||||
Authors | Ahn, J. / Zhang, Y. / Vann, K.R. / Kutateleadze, T. | ||||||
Citation | Journal: Structure / Year: 2019 Title: MORC3 Is a Target of the Influenza A Viral Protein NS1. Authors: Zhang, Y. / Ahn, J. / Green, K.J. / Vann, K.R. / Black, J. / Brooke, C.B. / Kutateladze, T.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o5w.cif.gz | 29.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o5w.ent.gz | 17 KB | Display | PDB format |
PDBx/mmJSON format | 6o5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o5w_validation.pdf.gz | 407.7 KB | Display | wwPDB validaton report |
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Full document | 6o5w_full_validation.pdf.gz | 407.7 KB | Display | |
Data in XML | 6o5w_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 6o5w_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/6o5w ftp://data.pdbj.org/pub/pdb/validation_reports/o5/6o5w | HTTPS FTP |
-Related structure data
Related structure data | 5svxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6792.451 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NS1-linked peptide (225-230) Linker(403-406) MORC Family CW-Type Zinc Finger 3(407-455) Source: (gene. exp.) Homo sapiens (human) / Gene: MORC3, KIAA0136, NXP2, ZCWCC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14149 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.58 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES pH 7.5 and 1.4M Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.28 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Aug 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→50 Å / Num. obs: 71940 / % possible obs: 99.2 % / Redundancy: 11 % / Rsym value: 0.08 / Net I/σ(I): 92.4 |
Reflection shell | Resolution: 1.41→1.43 Å / Num. unique obs: 554 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: 5SVX Resolution: 1.412→26.338 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 14.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.412→26.338 Å
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Refine LS restraints |
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LS refinement shell |
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