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Yorodumi- PDB-5z98: Crystal Structure of the Primate APOBEC3H Dimer mediated by RNA Duplex -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z98 | ||||||
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Title | Crystal Structure of the Primate APOBEC3H Dimer mediated by RNA Duplex | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN/RNA / APOBEC3 / APOBEC3H / cytidine deaminase / deaminase / anti-HIV / Vif / dsRNA / cancer / HIV-1 / SIV / chimpanzee / dimerization / Pan troglodytes / ANTIVIRAL PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pan troglodytes (chimpanzee) unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Matsuoka, T. / Nagae, T. / Ode, H. / Watanabe, N. / Iwatani, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Structural basis of chimpanzee APOBEC3H dimerization stabilized by double-stranded RNA. Authors: Matsuoka, T. / Nagae, T. / Ode, H. / Awazu, H. / Kurosawa, T. / Hamano, A. / Matsuoka, K. / Hachiya, A. / Imahashi, M. / Yokomaku, Y. / Watanabe, N. / Iwatani, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z98.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z98.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 5z98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z98_validation.pdf.gz | 471.3 KB | Display | wwPDB validaton report |
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Full document | 5z98_full_validation.pdf.gz | 477.6 KB | Display | |
Data in XML | 5z98_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 5z98_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/5z98 ftp://data.pdbj.org/pub/pdb/validation_reports/z9/5z98 | HTTPS FTP |
-Related structure data
Related structure data | 5w3vS 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: 21912.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pan troglodytes (chimpanzee) / Gene: APOBEC3H / Production host: Escherichia coli (E. coli) / References: UniProt: B7T0U6 #2: RNA chain | | Mass: 3192.948 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) #3: RNA chain | | Mass: 3159.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) #4: Chemical | #5: 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: 2.54 Å3/Da / Density % sol: 51.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 3350, 100mM ammonium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→43.49 Å / Num. obs: 24557 / % possible obs: 97.3 % / Redundancy: 3.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2074 / CC1/2: 0.876 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5w3v Resolution: 2.2→43.485 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 42.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→43.485 Å
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Refine LS restraints |
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LS refinement shell |
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