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Yorodumi- PDB-6j5d: Complex structure of MAb 4.2-scFv with louping ill virus envelope... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j5d | ||||||
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Title | Complex structure of MAb 4.2-scFv with louping ill virus envelope protein Domain III | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / protective and neutralizing antibody / flavivirus envelope protein / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane Similarity search - Function | ||||||
Biological species | Louping ill virus Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yang, X. / Qi, J. / Peng, R. / Dai, L. / Gould, E.A. / Tien, P. / Gao, G.F. | ||||||
Citation | Journal: J. Virol. / Year: 2019 Title: Molecular Basis of a Protective/Neutralizing Monoclonal Antibody Targeting Envelope Proteins of both Tick-Borne Encephalitis Virus and Louping Ill Virus. Authors: Yang, X. / Qi, J. / Peng, R. / Dai, L. / Gould, E.A. / Gao, G.F. / Tien, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j5d.cif.gz | 153.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j5d.ent.gz | 119.8 KB | Display | PDB format |
PDBx/mmJSON format | 6j5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j5d_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
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Full document | 6j5d_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 6j5d_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 6j5d_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/6j5d ftp://data.pdbj.org/pub/pdb/validation_reports/j5/6j5d | HTTPS FTP |
-Related structure data
Related structure data | 6j5cC 6j5fC 6j5gC 1svbS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 10977.397 Da / Num. of mol.: 1 / Fragment: Domain III Source method: isolated from a genetically manipulated source Source: (gene. exp.) Louping ill virus / Gene: envelope Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O40970 |
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#2: Antibody | Mass: 13169.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
#3: Antibody | Mass: 11977.288 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
#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: 3.12 Å3/Da / Density % sol: 60.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na HEPES pH 7.5, 1.6M K/Na phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 42003 / % possible obs: 99.7 % / Redundancy: 13.1 % / Biso Wilson estimate: 25.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4127 / CC1/2: 0.949 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SVB Resolution: 1.8→40.261 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→40.261 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 19.8781 Å / Origin y: 15.6949 Å / Origin z: 31.6553 Å
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Refinement TLS group | Selection details: all |