6JO8

The complex structure of CHIKV envelope glycoprotein bound to human MXRA8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 

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This is version 2.1 of the entry. See complete history


Literature

Molecular Basis of Arthritogenic Alphavirus Receptor MXRA8 Binding to Chikungunya Virus Envelope Protein.

Song, H.Zhao, Z.Chai, Y.Jin, X.Li, C.Yuan, F.Liu, S.Gao, Z.Wang, H.Song, J.Vazquez, L.Zhang, Y.Tan, S.Morel, C.M.Yan, J.Shi, Y.Qi, J.Gao, F.Gao, G.F.

(2019) Cell 177: 1714-1724.e12

  • DOI: https://doi.org/10.1016/j.cell.2019.04.008
  • Primary Citation of Related Structures:  
    6JO7, 6JO8

  • PubMed 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 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.


  • Organizational Affiliation

    Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Togavirin
A, C, E
406Chikungunya virusMutation(s): 0 
EC: 3.4.21.90
UniProt
Find proteins for C8YZ73 (Chikungunya virus)
Explore C8YZ73 
Go to UniProtKB:  C8YZ73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC8YZ73
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CHIKV E1
B, D, F
432Chikungunya virusMutation(s): 0 
UniProt
Find proteins for A4L787 (Chikungunya virus)
Explore A4L787 
Go to UniProtKB:  A4L787
Entity Groups  
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UniProt GroupA4L787
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix remodeling-associated protein 8G [auth M],
H [auth N],
I [auth O]
269Homo sapiensMutation(s): 0 
Gene Names: MXRA8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRK3 (Homo sapiens)
Explore Q9BRK3 
Go to UniProtKB:  Q9BRK3
PHAROS:  Q9BRK3
GTEx:  ENSG00000162576 
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UniProt GroupQ9BRK3
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth G],
K [auth H],
L [auth I]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG
GlyCosmos:  G07375KG
GlyGen:  G07375KG
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.79α = 90
b = 208.79β = 90
c = 299.739γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary