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- PDB-8ua4: Structure of eastern equine encephalitis virus VLP in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8ua4
TitleStructure of eastern equine encephalitis virus VLP in complex with VLDLR LA1
Components
  • (Envelope glycoprotein ...) x 3
  • Capsid protein
  • Very low-density lipoprotein receptor
KeywordsVIRUS LIKE PARTICLE / Alphaviruses / Receptor
Function / homology
Function and homology information


reelin receptor activity / glycoprotein transport / VLDL clearance / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / Reelin signalling pathway / very-low-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / togavirin ...reelin receptor activity / glycoprotein transport / VLDL clearance / very-low-density lipoprotein particle receptor activity / ventral spinal cord development / Reelin signalling pathway / very-low-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / togavirin / reelin-mediated signaling pathway / very-low-density lipoprotein particle / cargo receptor activity / positive regulation of dendrite development / T=4 icosahedral viral capsid / lipid transport / dendrite morphogenesis / regulation of synapse assembly / apolipoprotein binding / cholesterol metabolic process / VLDLR internalisation and degradation / clathrin-coated pit / receptor-mediated endocytosis / memory / calcium-dependent protein binding / nervous system development / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / receptor complex / symbiont-mediated suppression of host gene expression / lysosomal membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / calcium ion binding / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / glutamatergic synapse / virion membrane / structural molecule activity / signal transduction / proteolysis / RNA binding / membrane / plasma membrane
Similarity search - Function
: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein ...: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Low-density lipoprotein receptor domain class A / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / 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 / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein / Very low-density lipoprotein receptor / Structural polyprotein
Similarity search - Component
Biological speciesEastern equine encephalitis virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsAbraham, J. / Yang, P. / Li, W. / Fan, X. / Pan, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Burroughs Wellcome Fund United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for VLDLR recognition by eastern equine encephalitis virus.
Authors: Pan Yang / Wanyu Li / Xiaoyi Fan / Junhua Pan / Colin J Mann / Haley Varnum / Lars E Clark / Sarah A Clark / Adrian Coscia / Himanish Basu / Katherine Nabel Smith / Vesna Brusic / Jonathan Abraham /
Abstract: Eastern equine encephalitis virus (EEEV) is the most virulent alphavirus that infects humans, and many survivors develop neurological sequelae, including paralysis and intellectual disability. ...Eastern equine encephalitis virus (EEEV) is the most virulent alphavirus that infects humans, and many survivors develop neurological sequelae, including paralysis and intellectual disability. Alphavirus spike proteins comprise trimers of heterodimers of glycoproteins E2 and E1 that mediate binding to cellular receptors and fusion of virus and host cell membranes during entry. We recently identified very-low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2) as cellular receptors for EEEV and a distantly related alphavirus, Semliki Forest virus (SFV). Here, we use single-particle cryo-electron microscopy (cryo-EM) to determine structures of the EEEV and SFV spike glycoproteins bound to the VLDLR ligand-binding domain and found that EEEV and SFV interact with the same cellular receptor through divergent binding modes. Our studies suggest that the ability of LDLR-related proteins to interact with viral spike proteins through very small footprints with flexible binding modes results in a low evolutionary barrier to the acquisition of LDLR-related proteins as cellular receptors for diverse sets of viruses.
History
DepositionSep 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
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Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein E1
B: Envelope glycoprotein E2
C: Capsid protein
D: Envelope glycoprotein E1
E: Envelope glycoprotein E2
F: Capsid protein
G: Envelope glycoprotein E1
H: Envelope glycoprotein E2
I: Capsid protein
J: Envelope glycoprotein E1
K: Envelope glycoprotein E2
L: Capsid protein
M: Envelope glycoprotein E3
N: Envelope glycoprotein E3
O: Envelope glycoprotein E3
P: Envelope glycoprotein E3
R: Very low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)532,42830
Polymers529,73317
Non-polymers2,69513
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Envelope glycoprotein ... , 3 types, 12 molecules ADGJBEHKMNOP

#1: Protein
Envelope glycoprotein E1


Mass: 47984.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Eastern equine encephalitis virus strain PE6 mature envelope glycoprotein E1
Source: (gene. exp.) Eastern equine encephalitis virus / Strain: PE6 / Gene: E1 / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: Q88678
#2: Protein
Envelope glycoprotein E2


Mass: 47047.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Eastern equine encephalitis virus strain PE6 mature envelope glycoprotein E2
Source: (gene. exp.) Eastern equine encephalitis virus / Strain: PE6 / Gene: E2 / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: Q88678, togavirin
#4: Protein
Envelope glycoprotein E3


Mass: 7219.331 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eastern equine encephalitis virus / Strain: PE6 / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: P08768

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Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 18 molecules CFILR

#3: Protein
Capsid protein


Mass: 29178.846 Da / Num. of mol.: 4 / Mutation: K67N
Source method: isolated from a genetically manipulated source
Details: Eastern equine encephalitis virus mature capsid protein K67N mutant
Source: (gene. exp.) Eastern equine encephalitis virus / Strain: PE6 / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: Q88678
#5: Protein/peptide Very low-density lipoprotein receptor


Mass: 4015.421 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: human very low-density lipoprotein receptor (VLDLR) LA1
Source: (gene. exp.) Homo sapiens (human) / Gene: VLDLR / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: P98155
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Eastern equine encephalitis virusVIRUS#1-#50RECOMBINANT
2EEEV strain PE6 mature glycoprotein E1COMPLEX#11RECOMBINANT
3EEEV strain PE6 mature glycoprotein E2COMPLEX#21RECOMBINANT
4EEEV strain PE6 mature glycoprotein E3COMPLEX#41RECOMBINANT
5EEEV strain PE6 mature capsid proteinCOMPLEX#31RECOMBINANT
6VLDLRCOMPLEX#51RECOMBINANTEEEV receptor VLDLR
Molecular weight
IDEntity assembly-IDExperimental value
11
22
33NO
44NO
55NO
66NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Eastern equine encephalitis virus11021
32Eastern equine encephalitis virus11021
43Eastern equine encephalitis virus11021
54Eastern equine encephalitis virus11021
65Eastern equine encephalitis virus11021
76Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
54Homo sapiens (human)9606
65Homo sapiens (human)9606
76Homo sapiens (human)9606
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural host
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens9606
22Homo sapiens9606
33Homo sapiens9606
44Homo sapiens9606
55Homo sapiens9606
66Homo sapiens9606
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185420 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01334319
ELECTRON MICROSCOPYf_angle_d1.26546780
ELECTRON MICROSCOPYf_dihedral_angle_d8.4564704
ELECTRON MICROSCOPYf_chiral_restr0.0715247
ELECTRON MICROSCOPYf_plane_restr0.0126017

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