6NK3 | pdb_00006nk3

Crystal structure of murine Mxra8 ectodomain

• PDB DOI: https://doi.org/10.2210/pdb6NK3/pdb

• Classification: CELL INVASION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-04 Released: 2019-05-22 
• Deposition Author(s): Fremont, D.H., Kim, A.S., Nelson, C.A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.226 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

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

• PubMed: 31080061 
• DOI: https://doi.org/10.1016/j.cell.2019.04.006
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA.
Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA.
PaxVax, San Diego, CA 92121, USA.
Department of Chemistry, Washington University, Saint Louis, MO 63110, USA.
Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA. Electronic address: [e-mail].
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: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 62.33 kDa 
• Atom Count: 4,523 
• Modeled Residue Count: 528 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix remodeling-associated protein 8	A, B	274	Mus musculus	Mutation(s): 0  Gene Names: Mxra8, Asp3, Dicam
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DBV4 (Mus musculus) Explore Q9DBV4  Go to UniProtKB:  Q9DBV4
IMPC:  MGI:1922011

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.226 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.55	α = 90
b = 142.7	β = 90
c = 195.38	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): Fremont, D.H., Kim, A.S., Nelson, C.A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

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: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-23
  Changes: Structure summary