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- EMDB-9395: Electron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxr... -

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Basic information

Entry
Database: EMDB / ID: EMD-9395
TitleElectron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxra8 Receptor
Map data
SampleChikungunya virus with Mxra8 receptor:
Chikungunya virusChikungunya / mouse Mxra8 receptor ectodomain / E1 glycoprotein / E2 glycoprotein / Capsid proteinCapsid / E3 glycoprotein / Matrix remodeling-associated protein 8 / ligand
Function / homology
Function and homology information


Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / establishment of glial blood-brain barrier / togavirin / ciliary membrane / bicellular tight junction / host cell membrane / viral capsid / fusion of virus membrane with host endosome membrane / host cell cytoplasm ...Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / establishment of glial blood-brain barrier / togavirin / ciliary membrane / bicellular tight junction / host cell membrane / viral capsid / fusion of virus membrane with host endosome membrane / host cell cytoplasm / cell adhesion / virion attachment to host cell / virion membrane / serine-type endopeptidase activity / structural molecule activity / cell surface / integral component of membrane / nucleus / cytoplasm
Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin V-set domain / Peptidase S1, PA clan / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin subtype / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E2 glycoprotein ...Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin V-set domain / Peptidase S1, PA clan / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin subtype / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E2 glycoprotein / Peptidase S3, togavirin / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain B / Alphavirus E2 glycoprotein, domain C / Matrix remodeling-associated protein 8 / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Immunoglobulin V-set domain / Ig-like domain profile. / Alphavirus core protein (CP) domain profile. / Immunoglobulin E-set
Togavirin / Togavirin / Matrix remodeling-associated protein 8
Biological speciesChikungunya virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.99 Å
AuthorsBasore K / Kim AS / Nelson CA / Fremont DH / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesHHSN272201700060C United States
CitationJournal: Cell / Year: 2019
Title: Cryo-EM Structure of Chikungunya Virus in Complex with the Mxra8 Receptor.
Authors: Katherine Basore / Arthur S Kim / Christopher A Nelson / Rong Zhang / Brittany K Smith / Carla Uranga / Lo Vang / Ming Cheng / Michael L Gross / Jonathan Smith / Michael S Diamond / Daved H Fremont /
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 ...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.
Validation ReportPDB-ID: 6nk7

SummaryFull reportAbout validation report
History
DepositionJan 4, 2019-
Header (metadata) releaseFeb 27, 2019-
Map releaseMay 22, 2019-
UpdateJun 26, 2019-
Current statusJun 26, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6nk7
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6nk7
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9395.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 600 pix.
= 841.8 Å
1.4 Å/pix.
x 600 pix.
= 841.8 Å
1.4 Å/pix.
x 600 pix.
= 841.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.403 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-4.306646 - 6.398281
Average (Standard dev.)0.14662306 (±0.7393429)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 841.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4031.4031.403
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z841.800841.800841.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S123
start NC/NR/NS-300-300-300
NC/NR/NS600600600
D min/max/mean-4.3076.3980.147

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Supplemental data

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Sample components

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Entire Chikungunya virus with Mxra8 receptor

EntireName: Chikungunya virus with Mxra8 receptor / Number of components: 9

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Component #1: protein, Chikungunya virus with Mxra8 receptor

ProteinName: Chikungunya virus with Mxra8 receptor / Recombinant expression: No

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Component #2: protein, Chikungunya virus

ProteinName: Chikungunya virusChikungunya / Recombinant expression: No
SourceSpecies: Chikungunya virus / Strain: 181/25
Source (engineered)Expression System: Chlorocebus aethiops (grivet) / Cell of expression system: Vero

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Component #3: protein, mouse Mxra8 receptor ectodomain

ProteinName: mouse Mxra8 receptor ectodomain / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293

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Component #4: protein, E1 glycoprotein

ProteinName: E1 glycoprotein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 47.497906 kDa
SourceSpecies: Chikungunya virus / Strain: 181/25
Source (engineered)Expression System: Chlorocebus aethiops (grivet)

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Component #5: protein, E2 glycoprotein

ProteinName: E2 glycoprotein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 47.077719 kDa
SourceSpecies: Chikungunya virus / Strain: 181/25
Source (engineered)Expression System: Chlorocebus aethiops (grivet)

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Component #6: protein, Capsid protein

ProteinName: Capsid proteinCapsid / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 16.428607 kDa
SourceSpecies: Chikungunya virus / Strain: 181/25
Source (engineered)Expression System: Chlorocebus aethiops (grivet)

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Component #7: protein, E3 glycoprotein

ProteinName: E3 glycoprotein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 6.95507 kDa
SourceSpecies: Chikungunya virus / Strain: 181/25
Source (engineered)Expression System: Chlorocebus aethiops (grivet)

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Component #8: protein, Matrix remodeling-associated protein 8

ProteinName: Matrix remodeling-associated protein 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.022596 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionBuffer solution: Mxra8 at pH 7.4 / pH: 7.2
Support film0.458 mbar.l/s O2 and 0.11 mbar.l/s H2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 8357
3D reconstructionSoftware: cisTEM / Resolution: 4.99 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 3N42, 3N42, 3J0C, 3J0C, 5H23, 6NK3, 3N42
Chain ID: B, F, A, B, A, A, A
Output model

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