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- PDB-8ewf: CryoEM structure of Western equine encephalitis virus VLP in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ewf | ||||||
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Title | CryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor | ||||||
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![]() | VIRAL PROTEIN / WEEV / MXRA8 / Receptor / Alphavirus / Avian / VLP / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structural Genomics of Infectious Diseases / CSGID / VIRUS LIKE PARTICLE | ||||||
Function / homology | ![]() togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å | ||||||
![]() | Zimmerman, M.I. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Alternate domain repeat usage in an alphavirus entry receptor enables host species expansion Authors: Zimmerman, O. / Zimmerman, M.I. / Nelson, C.A. / Raju, S. / Errico, J.M. / Madden, E.A. / Hassan, A.O. / VanBlargan, L.A. / Kim, A.S. / Adams, L.J. / Basore, K. / Whitener, B.M. / Earnest, J. ...Authors: Zimmerman, O. / Zimmerman, M.I. / Nelson, C.A. / Raju, S. / Errico, J.M. / Madden, E.A. / Hassan, A.O. / VanBlargan, L.A. / Kim, A.S. / Adams, L.J. / Basore, K. / Whitener, B.M. / Earnest, J.T. / Holmes, A.C. / Ebel, G.D. / Zmasek, C. / Scheuermann, R.H. / Fremont, D.H. / Diamond, M.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 974.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 115.5 KB | Display | |
Data in CIF | ![]() | 168 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 28644MC ![]() 8danC 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: 47346.715 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 46858.312 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | | Mass: 30539.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Sugar | ChemComp-NAG / Has ligand of interest | Y | |
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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: Chikungunya virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2) Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 495 kDa/nm / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 1.03 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: cryoSPARC / Version: 4.01 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 745448 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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