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Yorodumi- PDB-6plk: Crystal structure of ZIKV-116 Fab in complex with ZIKV envelope DIII -
+Open data
-Basic information
Entry | Database: PDB / ID: 6plk | ||||||
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Title | Crystal structure of ZIKV-116 Fab in complex with ZIKV envelope DIII | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN / Human antibody / ZIKV-DIII / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / molecular adaptor activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / centrosome / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / GTP binding / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Zhao, H. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Exp.Med. / Year: 2020 Title: Mechanism of differential Zika and dengue virus neutralization by a public antibody lineage targeting the DIII lateral ridge. Authors: Zhao, H. / Xu, L. / Bombardi, R. / Nargi, R. / Deng, Z. / Errico, J.M. / Nelson, C.A. / Dowd, K.A. / Pierson, T.C. / Crowe, J.E. / Diamond, M.S. / Fremont, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6plk.cif.gz | 226.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6plk.ent.gz | 179.3 KB | Display | PDB format |
PDBx/mmJSON format | 6plk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/6plk ftp://data.pdbj.org/pub/pdb/validation_reports/pl/6plk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23990.951 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae gen. sp. (mammal) #2: Antibody | Mass: 23548.236 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae gen. sp. (mammal) #3: Protein | Mass: 11935.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X9PPI0, UniProt: A0A024B7W1*PLUS #4: 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: 2.47 Å3/Da / Density % sol: 50.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% MPD, 0.1 M Imidazole and 10% PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 50016 / % possible obs: 97.5 % / Redundancy: 6.5 % / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.3→2.344 Å / Num. unique obs: 2471 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KVG and 5GZO Resolution: 2.3→44.903 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→44.903 Å
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Refine LS restraints |
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LS refinement shell |
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