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- EMDB-9394: Electron Cryo-Microscopy Of Chikungunya VLP in complex with mouse... -

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Basic information

Entry
Database: EMDB / ID: EMD-9394
TitleElectron Cryo-Microscopy Of Chikungunya VLP in complex with mouse Mxra8 receptor
Map data
SampleChikungunya virus like particle with Mxra8:
Chikungunya virus like particle / Mxra8 receptor / Matrix remodeling-associated protein 8 / E1 glycoprotein / E2 glycoprotein / Capsid proteinCapsid / 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 / ec:3.4.21.90: / T=4 icosahedral viral capsid / ciliary membrane / bicellular tight junction / fusion of virus membrane with host endosome membrane / host cell cytoplasm / cell adhesion ...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 / ec:3.4.21.90: / T=4 icosahedral viral capsid / ciliary membrane / bicellular tight junction / fusion of virus membrane with host endosome membrane / host cell cytoplasm / cell adhesion / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / serine-type endopeptidase activity / structural molecule activity / cell surface / RNA binding / integral component of membrane / nucleus / cytoplasm
Alphavirus E1 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin-like domain / Immunoglobulin subtype / Immunoglobulin-like fold / Alphavirus E3 spike glycoprotein / Alphavirus E2 glycoprotein / Peptidase S3, togavirin / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Immunoglobulin E-set ...Alphavirus E1 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin-like domain / Immunoglobulin subtype / Immunoglobulin-like fold / Alphavirus E3 spike glycoprotein / Alphavirus E2 glycoprotein / Peptidase S3, togavirin / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Immunoglobulin E-set / Immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Alphavirus E2 glycoprotein, domain A / Immunoglobulin V-set domain / Alphavirus E2 glycoprotein, domain B / Alphavirus E2 glycoprotein, domain C / 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. / Peptidase S1, PA clan
Structural polyprotein / Matrix remodeling-associated protein 8
Biological speciesChikungunya virus (strain 37997) / Mus musculus (house mouse) / Chikungunya virus strain Senegal 37997
Methodsingle particle reconstruction / cryo EM / Resolution: 4.06 Å
AuthorsBasore K / Kim AS / Nelson CA / Fremont DH / Center for Structural Genomics of Infectious Diseases (CSGID)
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: 6nk6

SummaryFull reportAbout validation report
DateDeposition: Jan 4, 2019 / Header (metadata) release: Feb 27, 2019 / Map release: May 22, 2019 / Update: May 29, 2019

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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-6nk6
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6nk6
  • 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_9394.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-3.9830904 - 6.3030233
Average (Standard dev.)0.05519889 (±0.63631827)
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-3.9836.3030.055

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Supplemental data

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Sample components

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Entire Chikungunya virus like particle with Mxra8

EntireName: Chikungunya virus like particle with Mxra8
Details: VLP Produced by PaxVax Corporation, Redwood CA, USA. Mouse Mxra8 produced in HEK293 cells.
Number of components: 8

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Component #1: protein, Chikungunya virus like particle with Mxra8

ProteinName: Chikungunya virus like particle with Mxra8
Details: VLP Produced by PaxVax Corporation, Redwood CA, USA. Mouse Mxra8 produced in HEK293 cells.
Recombinant expression: No

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Component #2: protein, Chikungunya virus like particle

ProteinName: Chikungunya virus like particle / Recombinant expression: No
SourceSpecies: Chikungunya virus (strain 37997) / Strain: 37997
Source (engineered)Expression System: Homo sapiens (human) / Strain: HEK293F

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Component #3: protein, Mxra8 receptor

ProteinName: Mxra8 receptor / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human) / Strain: HEK293F

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Component #4: protein, Matrix remodeling-associated protein 8

ProteinName: Matrix remodeling-associated protein 8 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 30.819457 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, E1 glycoprotein

ProteinName: E1 glycoprotein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 47.346715 kDa
SourceSpecies: Chikungunya virus strain Senegal 37997 / Strain: 37997
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, E2 glycoprotein

ProteinName: E2 glycoprotein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 46.858312 kDa
SourceSpecies: Chikungunya virus strain Senegal 37997 / Strain: 37997
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, Capsid protein

ProteinName: Capsid proteinCapsid / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 16.458701 kDa
SourceSpecies: Chikungunya virus strain Senegal 37997 / Strain: 37997
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 12 / 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 solutionSpecimen conc.: 0.33 mg/mL / pH: 7.4
Support film0.458 mbar.l/s O2 and 0.11 mbar.l/s H2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 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: 22486
3D reconstructionSoftware: cisTEM / Resolution: 4.06 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
Chain ID: B, F, A, B, A, A
Output model

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