6NK6

Electron Cryo-Microscopy Of Chikungunya VLP in complex with mouse Mxra8 receptor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cryo-EM Structure of Chikungunya Virus in Complex with the Mxra8 Receptor.

Basore, K.Kim, A.S.Nelson, C.A.Zhang, R.Smith, B.K.Uranga, C.Vang, L.Cheng, M.Gross, M.L.Smith, J.Diamond, M.S.Fremont, D.H.

(2019) Cell 177: 1725

  • DOI: 10.1016/j.cell.2019.04.006
  • Primary Citation of Related Structures:  
    6NK3, 6NK6, 6NK5, 6NK7

  • PubMed 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 structure of Mxra8 and 4 to 5 Å resolution cryo-electron micr ...

    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.


    Organizational Affiliation

    Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA. Electronic address: fremont@wustl.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Matrix remodeling-associated protein 8MNOP269Mus musculusMutation(s): 0 
Gene Names: Mxra8Asp3Dicam
Find proteins for Q9DBV4 (Mus musculus)
Explore Q9DBV4 
Go to UniProtKB:  Q9DBV4
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
E2 glycoproteinEFGH419Chikungunya virus strain Senegal 37997Mutation(s): 0 
EC: 3.4.21.90
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997))
Explore Q5XXP3 
Go to UniProtKB:  Q5XXP3
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid proteinIJKL151Chikungunya virus strain Senegal 37997Mutation(s): 0 
EC: 3.4.21.90
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997))
Explore Q5XXP3 
Go to UniProtKB:  Q5XXP3
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E1 glycoproteinABCD439Chikungunya virus strain Senegal 37997Mutation(s): 0 
EC: 3.4.21.90
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997))
Explore Q5XXP3 
Go to UniProtKB:  Q5XXP3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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A, B, C, D, E, F, G, H, M, N, O, P
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary