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- EMDB-31568: Cryo-EM structure of VEEV VLP-LDLRAD3-D1 complex at the 2-fold axes -

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Basic information

Entry
Database: EMDB / ID: EMD-31568
TitleCryo-EM structure of VEEV VLP-LDLRAD3-D1 complex at the 2-fold axes
Map data
SampleVenezuelan equine encephalitis virus (strain TC-83)
  • LDLRAD3-D1
  • Capsid proteinCapsid
  • (Spike glycoprotein ...Spike protein) x 2
  • Low-density lipoprotein receptor class A domain-containing protein 3
  • assembly protein E3
  • ligand
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / regulation of protein processing / receptor-mediated endocytosis / amyloid-beta binding / suppression by virus of host gene expression / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / fusion of virus membrane with host endosome membrane / host cell cytoplasm ...togavirin / T=4 icosahedral viral capsid / regulation of protein processing / receptor-mediated endocytosis / amyloid-beta binding / suppression by virus of host gene expression / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / fusion of virus membrane with host endosome membrane / host cell cytoplasm / viral envelope / host cell nucleus / serine-type endopeptidase activity / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / integral component of membrane / plasma membrane
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 E1 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 E1 glycoprotein / Alphavirus E2 glycoprotein / Alphavirus E3 spike 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 glycoprotein, central and dimerisation domain superfamily / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like 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
Structural polyprotein / Low-density lipoprotein receptor class A domain-containing protein 3
Similarity search - Component
Biological speciesVenezuelan equine encephalitis virus (strain TC-83) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang X / Xiang Y / Ma J / Ma B / Huang C
CitationJournal: Nature / Year: 2021
Title: Structure of Venezuelan equine encephalitis virus with its receptor LDLRAD3.
Authors: Bingting Ma / Cuiqing Huang / Jun Ma / Ye Xiang / Xinzheng Zhang /
Abstract: Venezuelan equine encephalitis virus (VEEV) is an enveloped RNA virus that causes encephalitis and potentially mortality in infected humans and equines. At present, no vaccines or drugs are available ...Venezuelan equine encephalitis virus (VEEV) is an enveloped RNA virus that causes encephalitis and potentially mortality in infected humans and equines. At present, no vaccines or drugs are available that prevent or cure diseases caused by VEEV. Low-density lipoprotein receptor class A domain-containing 3 (LDLRAD3) was recently identified as a receptor for the entry of VEEV into host cells. Here we present the cryo-electron microscopy structure of the LDLRAD3 extracellular domain 1 (LDLRAD3-D1) in complex with VEEV virus-like particles at a resolution of 3.0 Å. LDLRAD3-D1 has a cork-like structure and is inserted into clefts formed between adjacent VEEV E2-E1 heterodimers in the viral-surface trimer spikes through hydrophobic and polar contacts. Mutagenesis studies of LDLRAD3-D1 identified residues that are involved in the key interactions with VEEV. Of note, some of the LDLRAD3-D1 mutants showed a significantly increased binding affinity for VEEV, suggesting that LDLRAD3-D1 may serve as a potential scaffold for the development of inhibitors of VEEV entry. Our structures provide insights into alphavirus assembly and the binding of receptors to alphaviruses, which may guide the development of therapeutic countermeasures against alphaviruses.
History
DepositionJul 23, 2021-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ffl
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ffl
  • 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_31568.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 337.92 Å
1.32 Å/pix.
x 256 pix.
= 337.92 Å
1.32 Å/pix.
x 256 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.0831546 - 0.13359044
Average (Standard dev.)0.00083491486 (±0.008295925)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.920337.920337.920
α/β/γ90.00090.00090.000
start NX/NY/NZ336210602
NX/NY/NZ227193139
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.0830.1340.001

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Supplemental data

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Sample components

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Entire Venezuelan equine encephalitis virus (strain TC-83)

EntireName: Venezuelan equine encephalitis virus (strain TC-83) / Number of Components: 9

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Component #1: protein, Venezuelan equine encephalitis virus (strain TC-83)

ProteinName: Venezuelan equine encephalitis virus (strain TC-83) / Recombinant expression: No
SourceSpecies: Venezuelan equine encephalitis virus (strain TC-83)

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Component #2: protein, Venezuelan equine encephalitis virus (strain TC-83)

ProteinName: Venezuelan equine encephalitis virus (strain TC-83) / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, LDLRAD3-D1

ProteinName: LDLRAD3-D1 / Recombinant expression: No

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Component #4: protein, Capsid protein

ProteinName: Capsid proteinCapsid / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 30.980801 kDa
SourceSpecies: Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Spike glycoprotein E1

ProteinName: Spike glycoprotein E1 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 47.952066 kDa
SourceSpecies: Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, Low-density lipoprotein receptor class A domain-containi...

ProteinName: Low-density lipoprotein receptor class A domain-containing protein 3
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 7.614737 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, assembly protein E3

ProteinName: assembly protein E3 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.488601 kDa
SourceSpecies: Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: protein, Spike glycoprotein E2

ProteinName: Spike glycoprotein E2 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 47.113746 kDa
SourceSpecies: Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 40 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 / Number of Projections: 894423
3D reconstructionResolution: 3.1 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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