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- PDB-8cxh: Structures of Zika Virus in Complex with Antibodies Targeting E D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cxh | ||||||||||||
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Title | Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy | ||||||||||||
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![]() | VIRUS/IMMUNE SYSTEM / ZIKV / scFv antibody / VIRUS-IMMUNE SYSTEM complex | ||||||||||||
Function / homology | ![]() low-density lipoprotein particle receptor binding / regulation of protein-containing complex assembly / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / histone deacetylase binding / double-stranded RNA binding / viral capsid / regulation of gene expression / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...low-density lipoprotein particle receptor binding / regulation of protein-containing complex assembly / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / histone deacetylase binding / double-stranded RNA binding / viral capsid / regulation of gene expression / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / cytoskeleton / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / ubiquitin protein ligase binding / host cell nucleus / virion attachment to host cell / protein kinase binding / structural molecule activity / virion membrane / protein-containing complex / proteolysis / extracellular region / ATP binding / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
![]() | Liu, W. / Zhang, X.K. / Gong, D.Y. / Dai, X.H. / Sharma, A. / Zhang, T.H. / Rey, F. / Zhou, Z.H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy Authors: Liu, W. / Zhang, X.K. / Gong, D.Y. / Dai, X.H. / Sharma, A. / Zhang, T.H. / Rey, F. / Zhou, Z.H. | ||||||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 566.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 60.1 KB | Display | |
Data in CIF | ![]() | 91.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27056MC ![]() 8cxgC ![]() 8cxiC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 69326.820 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 379600.719 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Model includes only small envelope protein M UNP residues 216-290 Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 14574.136 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Antibody | Mass: 11426.491 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Zika virus / Type: VIRUS / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION | ||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 26 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1094250 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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