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Yorodumi- PDB-6nk6: Electron Cryo-Microscopy Of Chikungunya VLP in complex with mouse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nk6 | ||||||
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Title | Electron Cryo-Microscopy Of Chikungunya VLP in complex with mouse Mxra8 receptor | ||||||
Components |
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Keywords | VIRUS LIKE PARTICLE/SIGNALING PROTEIN / Chikungunya / virus-like particle / viral receptor / Mxra8 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / VIRUS LIKE PARTICLE-SIGNALING PROTEIN complex | ||||||
Function / homology | Function and homology information establishment of glial blood-brain barrier / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / togavirin / T=4 icosahedral viral capsid / ciliary membrane / bicellular tight junction / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / cell differentiation ...establishment of glial blood-brain barrier / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / togavirin / T=4 icosahedral viral capsid / ciliary membrane / bicellular tight junction / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / cell differentiation / cell adhesion / 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 / structural molecule activity / virion membrane / cell surface / proteolysis / RNA binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Chikungunya virus strain Senegal 37997 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.06 Å | ||||||
Authors | Basore, K. / Kim, A.S. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell / Year: 2019 Title: Cryo-EM Structure of Chikungunya Virus in Complex with the Mxra8 Receptor. Authors: Katherine Basore / Arthur S Kim / Christopher A Nelson / Rong Zhang / Brittany K Smith / Carla Uranga / Lo Vang / Ming Cheng / Michael L Gross / Jonathan Smith / Michael S Diamond / Daved H Fremont / Abstract: Mxra8 is a receptor for multiple arthritogenic alphaviruses that cause debilitating acute and chronic musculoskeletal disease in humans. Herein, we present a 2.2 Å resolution X-ray crystal ...Mxra8 is a receptor for multiple arthritogenic alphaviruses that cause debilitating acute and chronic musculoskeletal disease in humans. Herein, we present a 2.2 Å resolution X-ray crystal structure of Mxra8 and 4 to 5 Å resolution cryo-electron microscopy reconstructions of Mxra8 bound to chikungunya (CHIKV) virus-like particles and infectious virus. The Mxra8 ectodomain contains two strand-swapped Ig-like domains oriented in a unique disulfide-linked head-to-head arrangement. Mxra8 binds by wedging into a cleft created by two adjacent CHIKV E2-E1 heterodimers in one trimeric spike and engaging a neighboring spike. Two binding modes are observed with the fully mature VLP, with one Mxra8 binding with unique contacts. Only the high-affinity binding mode was observed in the complex with infectious CHIKV, as viral maturation and E3 occupancy appear to influence receptor binding-site usage. Our studies provide insight into how Mxra8 binds CHIKV and creates a path for developing alphavirus entry inhibitors. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6nk6.cif.gz | 897.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nk6.ent.gz | 745.6 KB | Display | PDB format |
PDBx/mmJSON format | 6nk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nk6_validation.pdf.gz | 496.3 KB | Display | wwPDB validaton report |
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Full document | 6nk6_full_validation.pdf.gz | 564.6 KB | Display | |
Data in XML | 6nk6_validation.xml.gz | 114.9 KB | Display | |
Data in CIF | 6nk6_validation.cif.gz | 188.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/6nk6 ftp://data.pdbj.org/pub/pdb/validation_reports/nk/6nk6 | HTTPS FTP |
-Related structure data
Related structure data | 9394MC 9393C 9395C 6nk3C 6nk5C 6nk7C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 30819.457 Da / Num. of mol.: 4 / Fragment: ectodomain (UNP residues 39-291) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mxra8, Asp3, Dicam / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9DBV4 #2: Protein | Mass: 47346.715 Da / Num. of mol.: 4 / Fragment: UNP residues 810-1248 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3 #3: Protein | Mass: 46858.312 Da / Num. of mol.: 4 / Fragment: UNP residues 330-748 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3 #4: Protein | Mass: 16458.701 Da / Num. of mol.: 4 / Fragment: UNP residues 111-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3 #5: Sugar | ChemComp-NAG / |
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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
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Details of virus | Empty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.33 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 0.33 mg/mL VLP + 15 mg/mL Mxra8 | |||||||||||||||||||||||||||||||||||
Specimen support | Details: 0.458 mbar.l/s O2 and 0.11 mbar.l/s H2 / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 0.3 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22486 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||||||||||
Atomic model building |
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