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- PDB-8ys4: Overall structure of Eastern Equine Encephalitis virus VLP in com... -

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Basic information

Entry
Database: PDB / ID: 8ys4
TitleOverall structure of Eastern Equine Encephalitis virus VLP in complex with the receptor VLDLR LA3-5
Components
  • (Spike glycoprotein ...) x 2
  • (Very low-density lipoprotein ...) x 2
  • Capsid protein
KeywordsVIRUS LIKE PARTICLE / Eastern Equine Encephalitis virus / EEEV / receptor / complex / VLDLR / glycoprotein / VIRAL PROTEIN / alphavirus
Function / homology
Function and homology information


reelin receptor activity / VLDL clearance / glycoprotein transport / 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 / VLDL clearance / glycoprotein transport / 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 / positive regulation of dendrite development / cargo receptor activity / T=4 icosahedral viral capsid / lipid transport / dendrite morphogenesis / regulation of synapse assembly / apolipoprotein binding / cholesterol metabolic process / clathrin-coated pit / receptor-mediated endocytosis / VLDLR internalisation and degradation / 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 / virion membrane / glutamatergic synapse / 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
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: 4.8 Å
AuthorsCao, D. / Ma, B. / Cao, Z. / Xu, X. / Zhang, X. / Xiang, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2024
Title: The receptor VLDLR binds Eastern Equine Encephalitis virus through multiple distinct modes.
Authors: Duanfang Cao / Bingting Ma / Ziyi Cao / Xiaoyu Xu / Xinzheng Zhang / Ye Xiang /
Abstract: Eastern Equine Encephalitis virus (EEEV) is an alphavirus that can cause severe diseases in infected humans. The very low-density lipoprotein receptor (VLDLR) was recently identified as a receptor of ...Eastern Equine Encephalitis virus (EEEV) is an alphavirus that can cause severe diseases in infected humans. The very low-density lipoprotein receptor (VLDLR) was recently identified as a receptor of EEEV. Herein, we performed cryo-electron microscopy structural and biochemistry studies on the specific interactions between EEEV and VLDLR. Our results show that VLDLR binds EEEV at three different sites A, B and C through its membrane-distal LDLR class A (LA) repeats. Site A is located in the cleft in between the E1-E2 heterodimers. Site B is located near the connecting β ribbon of E2 and is in proximity to site A, while site C is on the domain B of E2. The binding of VLDLR LAs to EEEV is in complex modes, including the LA1-2 and LA3-5 mediated two major modes. Disruption of the LA1-2 mediated binding significantly affect the cell attachment of EEEV. However, the mutation W132G of VLDLR impairs the binding of LA3, drives the switch of the binding modes, and significantly enhances the attachment of EEEV to the cell. The W132G variant of VLDLR could be identified in human genome and SNP sequences, implying that people with similar mutations in VLDLR may be highly susceptible to EEEV infection.
History
DepositionMar 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jul 2, 2025Group: Data collection / Category: em_software / Item: _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)533,00728
Polymers532,68720
Non-polymers3218
Water00
1
A: Spike glycoprotein E1
B: Spike glycoprotein E2
C: Capsid protein
D: Spike glycoprotein E1
E: Spike glycoprotein E2
F: Capsid protein
G: Spike glycoprotein E1
H: Spike glycoprotein E2
I: Capsid protein
J: Spike glycoprotein E1
K: Spike glycoprotein E2
L: Capsid protein
M: Very low-density lipoprotein receptor
N: Very low-density lipoprotein receptor
O: Very low-density lipoprotein receptor
P: Very low-density lipoprotein receptor
Q: Very low-density lipoprotein receptor
R: Very low-density lipoprotein receptor
S: Very low-density lipoprotein receptor
T: Very low-density lipoprotein receptor
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)31,980,4321680
Polymers31,961,1951200
Non-polymers19,237480
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

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Spike glycoprotein ... , 2 types, 8 molecules ADGJBEHK

#1: Protein
Spike glycoprotein E1 / E1 envelope glycoprotein


Mass: 47984.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eastern equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: Q4QXJ7
#2: Protein
Spike glycoprotein E2 / E2 envelope glycoprotein


Mass: 47047.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eastern equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: Q4QXJ7

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Very low-density lipoprotein ... , 2 types, 8 molecules MNOPQRST

#4: Protein/peptide
Very low-density lipoprotein receptor / VLDL receptor / VLDL-R


Mass: 4428.696 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VLDLR / Production host: Homo sapiens (human) / References: UniProt: P98155
#5: Protein/peptide
Very low-density lipoprotein receptor / VLDL receptor / VLDL-R


Mass: 4532.837 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VLDLR / Production host: Homo sapiens (human) / References: UniProt: P98155

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Protein / Non-polymers , 2 types, 12 molecules CFIL

#3: Protein
Capsid protein / Coat protein / C


Mass: 29178.846 Da / Num. of mol.: 4 / Mutation: K67N
Source method: isolated from a genetically manipulated source
Details: AAU95735.1 / Source: (gene. exp.) Eastern equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: Q4QXJ7, togavirin
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca

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Details

Has ligand of interestN
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

ComponentName: Eastern equine encephalitis virus / Type: VIRUS / Details: Virus like particle of EEEV / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Eastern equine encephalitis virus / Strain: PE6
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 8
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14840 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00434711
ELECTRON MICROSCOPYf_angle_d0.76947289
ELECTRON MICROSCOPYf_dihedral_angle_d11.3534719
ELECTRON MICROSCOPYf_chiral_restr0.0515240
ELECTRON MICROSCOPYf_plane_restr0.0086127

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