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Yorodumi- PDB-6uej: Crystal structure of human zinc finger antiviral protein bound to RNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uej | ||||||
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Title | Crystal structure of human zinc finger antiviral protein bound to RNA | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN / Zinc Finger Antiviral protein / ZAP / RNA binding domain | ||||||
Function / homology | Function and homology information positive regulation of RIG-I signaling pathway / positive regulation of mRNA catabolic process / negative regulation of viral genome replication / positive regulation of interferon-alpha production / positive regulation of type I interferon production / positive regulation of interferon-beta production / response to virus / Signaling by BRAF and RAF1 fusions / positive regulation of canonical NF-kappaB signal transduction / defense response to virus ...positive regulation of RIG-I signaling pathway / positive regulation of mRNA catabolic process / negative regulation of viral genome replication / positive regulation of interferon-alpha production / positive regulation of type I interferon production / positive regulation of interferon-beta production / response to virus / Signaling by BRAF and RAF1 fusions / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / cadherin binding / innate immune response / RNA binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Meagher, J.L. / Smith, J.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Structure of the zinc-finger antiviral protein in complex with RNA reveals a mechanism for selective targeting of CG-rich viral sequences. Authors: Meagher, J.L. / Takata, M. / Goncalves-Carneiro, D. / Keane, S.C. / Rebendenne, A. / Ong, H. / Orr, V.K. / MacDonald, M.R. / Stuckey, J.A. / Bieniasz, P.D. / Smith, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uej.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uej.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 6uej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/6uej ftp://data.pdbj.org/pub/pdb/validation_reports/ue/6uej | HTTPS FTP |
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-Related structure data
Related structure data | 6ueiC 3u9gS S: Starting model for refinement C: citing same article (ref.) |
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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: 25991.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZC3HAV1, ZC3HDC2, PRO1677 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z2W4 | ||||||
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#2: RNA chain | Mass: 911.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SPM / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.4 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 7% Peg 8000, 30mM magnesium chloride, 10mM spermine, 50mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9762 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 7, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→40.668 Å / Num. obs: 18081 / % possible obs: 99.8 % / Redundancy: 20.564 % / Biso Wilson estimate: 64.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.081 / Χ2: 1.087 / Net I/σ(I): 20.69 / Num. measured all: 371826 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U9G Resolution: 2.21→38 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.196 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.177
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Displacement parameters | Biso max: 167.22 Å2 / Biso mean: 75.67 Å2 / Biso min: 43.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.21→38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 47
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