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: https://doi.org/10.1016/j.cell.2019.04.006
  • Primary Citation of Related Structures:  
    6NK3, 6NK5, 6NK6, 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 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix remodeling-associated protein 8A [auth M],
B [auth N],
C [auth O],
D [auth P]
269Mus musculusMutation(s): 0 
Gene Names: Mxra8Asp3Dicam
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DBV4 (Mus musculus)
Explore Q9DBV4 
Go to UniProtKB:  Q9DBV4
IMPC:  MGI:1922011
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9DBV4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E1 glycoproteinE [auth A],
H [auth B],
K [auth C],
N [auth D]
439Chikungunya virus strain Senegal 37997Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997))
Explore Q5XXP3 
Go to UniProtKB:  Q5XXP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5XXP3
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
E2 glycoproteinF [auth E],
I [auth F],
L [auth G],
O [auth H]
419Chikungunya virus strain Senegal 37997Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997))
Explore Q5XXP3 
Go to UniProtKB:  Q5XXP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5XXP3
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid proteinG [auth I],
J,
M [auth K],
P [auth L]
151Chikungunya virus strain Senegal 37997Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997))
Explore Q5XXP3 
Go to UniProtKB:  Q5XXP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5XXP3
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth H]
Q [auth M]
R [auth N]
S [auth O]
AA [auth D],
BA [auth H],
Q [auth M],
R [auth N],
S [auth O],
T [auth P],
U [auth A],
V [auth E],
W [auth B],
X [auth F],
Y [auth C],
Z [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM1.0.0-beta
MODEL REFINEMENTPHENIX1.14

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • 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