+Open data
-Basic information
Entry | Database: PDB / ID: 7u4a | ||||||
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Title | Crystal Structure of Zika virus xrRNA1 mutant | ||||||
Components | RNA (70-MER) | ||||||
Keywords | RNA / xrRNA / Viral RNA / Flavivirus | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Zika virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Thompson, R.D. / Carbaugh, D.L. / Nielsen, J.R. / Witt, C. / Meganck, R.M. / Rangadurai, A. / Zhao, B. / Bonin, J.P. / Nathan, N.T. / Marzluff, W.F. ...Thompson, R.D. / Carbaugh, D.L. / Nielsen, J.R. / Witt, C. / Meganck, R.M. / Rangadurai, A. / Zhao, B. / Bonin, J.P. / Nathan, N.T. / Marzluff, W.F. / Frank, A.T. / Lazear, H.M. / Zhang, Q. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Dynamic Basis of Xrn1 Resistance in Mosquito-borne Flavivirus RNA Authors: Thompson, R.D. / Carbaugh, D.L. / Nielsen, J.R. / Witt, C. / Meganck, R.M. / Rangadurai, A. / Zhao, B. / Bonin, J.P. / Nathan, N.T. / Marzluff, W.F. / Frank, A.T. / Lazear, H.M. / Zhang, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u4a.cif.gz | 80.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u4a.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 7u4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/7u4a ftp://data.pdbj.org/pub/pdb/validation_reports/u4/7u4a | HTTPS FTP |
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-Related structure data
Related structure data | 5tpyS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 23325.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zika virus |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: RNA was exchanged and concentrated into 10 mM HEPES-KOH, pH 7.5, 2.5 mM magnesium chloride. After concentration to 7.5 mg/mL (~330 uM), RNA was diluted to 4 mg/mL, 100 mM spermidine was ...Details: RNA was exchanged and concentrated into 10 mM HEPES-KOH, pH 7.5, 2.5 mM magnesium chloride. After concentration to 7.5 mg/mL (~330 uM), RNA was diluted to 4 mg/mL, 100 mM spermidine was added to a final concentration of 0.5 mM. 0.5 uL RNA was added to 2 uL crystallization solution (50 mM sodium cacodylate, pH 6.0, 150 mM sodium chloride, 4 mM calcium chloride, 0.6 mM spermine, 36% 1,6-hexanediol) and crystallized via hanging drop vapor diffusion over 1 mL crystallization solution. Crystals formed within 24 hours at 20 degrees C and were harvested after 36 hours. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 9, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.15→33.2 Å / Num. obs: 4391 / % possible obs: 95.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 58.32 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.074 / Rrim(I) all: 0.136 / Net I/σ(I): 9.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5TPY Resolution: 3.15→33.2 Å / SU ML: 0.3436 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 19.4835 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 59.85 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→33.2 Å
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Refine LS restraints |
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LS refinement shell |
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