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Yorodumi- PDB-6jo8: The complex structure of CHIKV envelope glycoprotein bound to hum... -
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-Basic information
Entry | Database: PDB / ID: 6jo8 | |||||||||
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Title | The complex structure of CHIKV envelope glycoprotein bound to human MXRA8 | |||||||||
Components |
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Keywords | VIRAL PROTEIN / Arthritogenic alphaviruses / receptor / MXRA8 / Chikungunya virus | |||||||||
Function / homology | Function and homology information establishment of glial blood-brain barrier / protein metabolic process => GO:0019538 / togavirin / T=4 icosahedral viral capsid / ciliary membrane / host cell membrane / bicellular tight junction / viral process / post-translational protein modification / Post-translational protein phosphorylation ...establishment of glial blood-brain barrier / protein metabolic process => GO:0019538 / togavirin / T=4 icosahedral viral capsid / ciliary membrane / host cell membrane / bicellular tight junction / viral process / post-translational protein modification / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / viral capsid / host cell cytoplasm / membrane => GO:0016020 / cell adhesion / endoplasmic reticulum lumen / 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 / cell surface / extracellular exosome / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Chikungunya virus Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.495 Å | |||||||||
Authors | Song, H. / Zhao, Z. / Qi, J. / Gao, F. / Gao, F.G. | |||||||||
Citation | Journal: Cell / Year: 2019 Title: Molecular Basis of Arthritogenic Alphavirus Receptor MXRA8 Binding to Chikungunya Virus Envelope Protein. Authors: Hao Song / Zhennan Zhao / Yan Chai / Xiyue Jin / Changyao Li / Fei Yuan / Sheng Liu / Zhengrong Gao / Haiyuan Wang / Jian Song / Leonardo Vazquez / Yanfang Zhang / Shuguang Tan / Carlos M ...Authors: Hao Song / Zhennan Zhao / Yan Chai / Xiyue Jin / Changyao Li / Fei Yuan / Sheng Liu / Zhengrong Gao / Haiyuan Wang / Jian Song / Leonardo Vazquez / Yanfang Zhang / Shuguang Tan / Carlos M Morel / Jinghua Yan / Yi Shi / Jianxun Qi / Feng Gao / George F Gao / Abstract: Arthritogenic alphaviruses, such as Chikungunya virus (CHIKV), cause severe and debilitating rheumatic diseases worldwide, resulting in severe morbidity and economic costs. Recently, MXRA8 was ...Arthritogenic alphaviruses, such as Chikungunya virus (CHIKV), cause severe and debilitating rheumatic diseases worldwide, resulting in severe morbidity and economic costs. Recently, MXRA8 was reported as an entry receptor. Here, we present the crystal structures of the mouse MXRA8, human MXRA8 in complex with the CHIKV E protein, and the cryo-electron microscopy structure of human MXRA8 and CHIKV virus-like particle. MXRA8 has two Ig-like domains with unique structural topologies. This receptor binds in the "canyon" between two protomers of the E spike on the surface of the virion. The atomic details at the interface between the two binding entities reveal that both the two domains and the hinge region of MXRA8 are involved in interaction with CHIKV E1-E2 residues from two protomers. Notably, the stalk region of MXRA8 is critical for CHIKV virus entry. This finding provides important information regarding the development of therapeutic countermeasures against those arthritogenic alphaviruses. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jo8.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6jo8.ent.gz | 1015.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jo8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6jo8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6jo8_validation.xml.gz | 104.5 KB | Display | |
Data in CIF | 6jo8_validation.cif.gz | 138.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/6jo8 ftp://data.pdbj.org/pub/pdb/validation_reports/jo/6jo8 | HTTPS FTP |
-Related structure data
Related structure data | 9857C 6jo7C 3n40S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 45882.105 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): high5 / References: UniProt: C8YZ73, togavirin #2: Protein | Mass: 46030.770 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): high5 / References: UniProt: A4L787 #3: Protein | Mass: 30148.695 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MXRA8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BRK3 #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.15 Å3/Da / Density % sol: 76.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.8M Ammomium phophate dibasic, 0.1M sodium acetate pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97893 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jul 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97893 Å / Relative weight: 1 |
Reflection | Resolution: 3.49→50.15 Å / Num. obs: 95731 / % possible obs: 100 % / Redundancy: 130.4 % / CC1/2: 0.999 / Rpim(I) all: 0.042 / Rsym value: 0.047 / Net I/σ(I): 21 |
Reflection shell | Resolution: 3.49→3.61 Å / Redundancy: 127 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9457 / CC1/2: 0.642 / Rpim(I) all: 0.802 / Rsym value: 0.9022 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3N40 Resolution: 3.495→50.15 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 497.11 Å2 / Biso mean: 202.241 Å2 / Biso min: 74.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.495→50.15 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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