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Yorodumi- PDB-6u8d: Crystal structure of hepatitis C virus IRES junction IIIabc in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u8d | |||||||||
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Title | Crystal structure of hepatitis C virus IRES junction IIIabc in complex with Fab HCV2 | |||||||||
Components |
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Keywords | RNA/Immune System / Internal ribosome entry site (IRES) / hepatitis C virus / Junction IIIabc / Antibody-assisted RNA crystallography / Viral translation / Viral RNA domains / RNA / RNA-Immune System complex | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | Homo sapiens (human) Hepacivirus C | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.807 Å | |||||||||
Authors | Koirala, D. / Lewicka, A. / Koldobskaya, Y. / Huang, H. / Piccirilli, J.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation. Authors: Koirala, D. / Lewicka, A. / Koldobskaya, Y. / Huang, H. / Piccirilli, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u8d.cif.gz | 276.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u8d.ent.gz | 217.5 KB | Display | PDB format |
PDBx/mmJSON format | 6u8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u8d_validation.pdf.gz | 248 KB | Display | wwPDB validaton report |
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Full document | 6u8d_full_validation.pdf.gz | 248 KB | Display | |
Data in XML | 6u8d_validation.xml.gz | 953 B | Display | |
Data in CIF | 6u8d_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/6u8d ftp://data.pdbj.org/pub/pdb/validation_reports/u8/6u8d | HTTPS FTP |
-Related structure data
Related structure data | 6u8kC 6mwnS 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: RNA chain | Mass: 22014.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: JIIIabc of hepatitis C virus IRES / Source: (synth.) Hepacivirus C |
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#2: Antibody | Mass: 25019.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Heavy chain of Fab HCV2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#3: Antibody | Mass: 23410.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Light chain of Fab HCV2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#4: 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: 2.69 Å3/Da / Density % sol: 54.29 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M ammonium acetate, 0.1 M bis-tris pH 5.5, 45% 2-methyl-2,4-pentanediaol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.807→61.362 Å / Num. obs: 67168 / % possible obs: 98.73 % / Redundancy: 3.9 % / Biso Wilson estimate: 40.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04042 / Rpim(I) all: 0.0232 / Rrim(I) all: 0.04674 / Net I/σ(I): 15.66 |
Reflection shell | Resolution: 1.807→1.872 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.134 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 6420 / CC1/2: 0.481 / Rpim(I) all: 0.6692 / % possible all: 94.58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Fab HAVx, 6MWN Resolution: 1.807→61.362 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 168.41 Å2 / Biso mean: 55.9495 Å2 / Biso min: 26.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.807→61.362 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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