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Yorodumi- PDB-8cxg: Structures of Zika Virus in Complex with Antibodies Targeting E D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cxg | ||||||||||||
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Title | Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy | ||||||||||||
Components |
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Keywords | VIRUS/IMMUNE SYSTEM / ZIKV / scFv antibody / VIRUS-IMMUNE SYSTEM complex | ||||||||||||
Function / homology | Function and homology information 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 / cytoskeleton / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / 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 | Homo sapiens (human) Zika virus | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Liu, W. / Zhang, X.K. / Gong, D.Y. / Dai, X.H. / Sharma, A. / Zhang, T.H. / Rey, F. / Zhou, Z.H. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published 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. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cxg.cif.gz | 606.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cxg.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8cxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cxg_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8cxg_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8cxg_validation.xml.gz | 63.8 KB | Display | |
Data in CIF | 8cxg_validation.cif.gz | 99 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/8cxg ftp://data.pdbj.org/pub/pdb/validation_reports/cx/8cxg | HTTPS FTP |
-Related structure data
Related structure data | 27055MC 8cxhC 8cxiC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Antibody | Mass: 13385.699 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 12081.482 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Protein | Mass: 69326.820 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus / Gene: ANKRA2, ANKRA / Production host: Homo sapiens (human) / References: UniProt: Q9H9E1, UniProt: A0A142DS37 #4: 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.) Zika virus / Production host: Homo sapiens (human) / References: UniProt: A0A1S6LXE0 |
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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 |
-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: Homo sapiens (human) | ||||||||||||
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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1007280 / Symmetry type: POINT |