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Yorodumi- PDB-8dan: CryoEM structure of Western equine encephalitis virus VLP in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dan | ||||||
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Title | CryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor | ||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / WEEV / MXRA8 / Receptor / Alphavirus / Avian / VLP / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information T=4 icosahedral viral capsid / host cell cytoplasm / cell adhesion / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane ...T=4 icosahedral viral capsid / host cell cytoplasm / cell adhesion / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Western equine encephalitis virus Asarcornis scutulata (bird) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.74 Å | ||||||
Authors | Zimmerman, M.I. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dan.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8dan.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 8dan.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/8dan ftp://data.pdbj.org/pub/pdb/validation_reports/da/8dan | HTTPS FTP |
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-Related structure data
Related structure data | 27271MC 8ewfC 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: Protein | Mass: 47188.562 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Western equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: Q1W679 #2: Protein | Mass: 46171.617 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Western equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: Q1W679 #3: Protein | Mass: 30615.361 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Asarcornis scutulata (bird) / Gene: Mxra8, ASASCU_R01628 / Production host: Homo sapiens (human) / References: UniProt: A0A7K7KW08 #4: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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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: Western equine encephalitis virus VLP in complex with avian MXRA8 receptor Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 495 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Western equine encephalitis virus |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
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) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 4.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250347 / Symmetry type: POINT |