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- EMDB-24116: CryoEM structure of Venezuelan equine encephalitis virus VLP in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-24116
TitleCryoEM structure of Venezuelan equine encephalitis virus VLP in complex with the LDLRAD3 receptor
Map data
SampleVenezuelan equine encephalitis VLP in complex with domain 1 of the LDLRAD3 receptor
  • LDLRAD3 receptor domain 1
  • Venezuelan equine encephalitis VLP
  • Low-density lipoprotein receptor class A domain-containing protein 3
  • E1 envelope glycoprotein
  • E2 envelope glycoprotein
  • Capsid
  • (ligand) x 2
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / regulation of protein processing / receptor-mediated endocytosis / amyloid-beta binding / virion attachment to host cell / fusion of virus membrane with host endosome membrane / host cell cytoplasm / serine-type endopeptidase activity / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / regulation of protein processing / receptor-mediated endocytosis / amyloid-beta binding / virion attachment to host cell / fusion of virus membrane with host endosome membrane / host cell cytoplasm / serine-type endopeptidase activity / host cell plasma membrane / virion membrane / structural molecule activity / membrane / integral component of membrane / plasma membrane / cytoplasm
Similarity search - Function
Peptidase S3, togavirin / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein, domain B / Alphavirus E2 glycoprotein, domain A / Alphavirus E3 spike glycoprotein ...Peptidase S3, togavirin / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein, domain B / Alphavirus E2 glycoprotein, domain A / Alphavirus E3 spike glycoprotein / Alphavirus E2 glycoprotein / Alphavirus E1 glycoprotein / LDL-receptor class A (LDLRA) domain signature. / Low-density lipoprotein (LDL) receptor class A, conserved site / Low-density lipoprotein receptor domain class A / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Togavirin / Low-density lipoprotein receptor class A domain-containing protein 3
Similarity search - Component
Biological speciesVenezuelan equine encephalitis virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsBasore K / 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 Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Nature / Year: 2021
Title: Structure of Venezuelan equine encephalitis virus in complex with the LDLRAD3 receptor.
Authors: Katherine Basore / Hongming Ma / Natasha M Kafai / Samantha Mackin / Arthur S Kim / Christopher A Nelson / Michael S Diamond / Daved H Fremont /
Abstract: LDLRAD3 is a recently defined attachment and entry receptor for Venezuelan equine encephalitis virus (VEEV), a New World alphavirus that causes severe neurological disease in humans. Here we present ...LDLRAD3 is a recently defined attachment and entry receptor for Venezuelan equine encephalitis virus (VEEV), a New World alphavirus that causes severe neurological disease in humans. Here we present near-atomic-resolution cryo-electron microscopy reconstructions of VEEV virus-like particles alone and in a complex with the ectodomains of LDLRAD3. Domain 1 of LDLRAD3 is a low-density lipoprotein receptor type-A module that binds to VEEV by wedging into a cleft created by two adjacent E2-E1 heterodimers in one trimeric spike, and engages domains A and B of E2 and the fusion loop in E1. Atomic modelling of this interface is supported by mutagenesis and anti-VEEV antibody binding competition assays. Notably, VEEV engages LDLRAD3 in a manner that is similar to the way that arthritogenic alphaviruses bind to the structurally unrelated MXRA8 receptor, but with a much smaller interface. These studies further elucidate the structural basis of alphavirus-receptor interactions, which could inform the development of therapies to mitigate infection and disease against multiple members of this family.
History
DepositionMay 27, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateNov 10, 2021-
Current statusNov 10, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7n1h
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7n1h
  • 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_24116.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 700 pix.
= 770. Å
1.1 Å/pix.
x 700 pix.
= 770. Å
1.1 Å/pix.
x 700 pix.
= 770. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.01069855 - 2.1788745
Average (Standard dev.)0.011070774 (±0.07157769)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-349-349-349
Dimensions700700700
Spacing700700700
CellA=B=C: 770.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z700700700
origin x/y/z0.0000.0000.000
length x/y/z770.000770.000770.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-349-349-349
NC/NR/NS700700700
D min/max/mean-0.0112.1790.011

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Supplemental data

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Additional map: Unsharpened electron microscopy map of Venezuelan equine encephalitis...

Fileemd_24116_additional_1.map
AnnotationUnsharpened electron microscopy map of Venezuelan equine encephalitis VLP in complex with domain 1 of LDLRAD3 receptor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unsharpened half map #1 of Venezuelan equine encephalitis...

Fileemd_24116_half_map_1.map
AnnotationUnsharpened half map #1 of Venezuelan equine encephalitis VLP in complex with domain 1 of LDLRAD3 receptor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unsharpened half map #2 of Venezuelan equine encephalitis...

Fileemd_24116_half_map_2.map
AnnotationUnsharpened half map #2 of Venezuelan equine encephalitis VLP in complex with domain 1 of LDLRAD3 receptor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Venezuelan equine encephalitis VLP in complex with domain 1 of th...

EntireName: Venezuelan equine encephalitis VLP in complex with domain 1 of the LDLRAD3 receptor
Number of Components: 9

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Component #1: protein, Venezuelan equine encephalitis VLP in complex with domai...

ProteinName: Venezuelan equine encephalitis VLP in complex with domain 1 of the LDLRAD3 receptor
Recombinant expression: No
SourceSpecies: Venezuelan equine encephalitis virus / Strain: TC-83
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293F

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Component #2: cellular-component, LDLRAD3 receptor domain 1

Cellular-componentName: LDLRAD3 receptor domain 1
Details: Receptor fragment produced asserted Fc fusion in Expi293F cells and released by HRV 3C Cleavage.
Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: Expi293F

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Component #3: protein, Venezuelan equine encephalitis VLP

ProteinName: Venezuelan equine encephalitis VLP
Details: Virus like particle produce in HEK293F cells by recombinant expression of structural proteins.
Recombinant expression: No
SourceSpecies: Venezuelan equine encephalitis virus / Strain: TC-83
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293F

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Component #4: protein, Low-density lipoprotein receptor class A domain-containi...

ProteinName: Low-density lipoprotein receptor class A domain-containing protein 3
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 4.312861 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, E1 envelope glycoprotein

ProteinName: E1 envelope glycoprotein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 47.952066 kDa
SourceSpecies: Venezuelan equine encephalitis virus
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, E2 envelope glycoprotein

ProteinName: E2 envelope glycoprotein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 47.113746 kDa
SourceSpecies: Venezuelan equine encephalitis virus
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, Capsid

ProteinName: Capsid / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 18.19584 kDa
SourceSpecies: Venezuelan equine encephalitis virus
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Component #9: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 8 / 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 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: 35 e/Å2 / Illumination Mode: SPOT SCAN
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: 12216
3D reconstructionSoftware: RELION / Resolution: 4.3 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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