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- EMDB-9857: Cryo-EM structure of Chikungunya VLP in complex with its receptor... -

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Basic information

Entry
Database: EMDB / ID: EMD-9857
TitleCryo-EM structure of Chikungunya VLP in complex with its receptor MXRA8
Map data
SampleChikungunya VLP complexed with its receptor MXRA8
SourceChikungunya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsSong H / Liu S / Gao GF
CitationJournal: 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 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.
DateDeposition: Mar 20, 2019 / Header (metadata) release: May 15, 2019 / Map release: May 15, 2019 / Update: May 15, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

FileDownload / File: emd_9857.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 340 pix.
= 918. Å
2.7 Å/pix.
x 340 pix.
= 918. Å
2.7 Å/pix.
x 340 pix.
= 918. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.058119792 - 0.073850326
Average (Standard dev.)0.00080194883 (±0.0053625233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 918.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z918.000918.000918.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0580.0740.001

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Supplemental data

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Sample components

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Entire Chikungunya VLP complexed with its receptor MXRA8

EntireName: Chikungunya VLP complexed with its receptor MXRA8 / Number of components: 1

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Component #1: protein, Chikungunya VLP complexed with its receptor MXRA8

ProteinName: Chikungunya VLP complexed with its receptor MXRA8 / Recombinant expression: No
SourceSpecies: Chikungunya virus / Strain: 119067
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: 293T

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 1596
3D reconstructionResolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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