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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 / VLDL clearance / glycoprotein transport / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / very-low-density lipoprotein particle binding / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance ...reelin receptor activity / VLDL clearance / glycoprotein transport / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / very-low-density lipoprotein particle binding / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / togavirin / very-low-density lipoprotein particle / positive regulation of dendrite development / T=4 icosahedral viral capsid / lipid transport / dendrite morphogenesis / cargo receptor activity / apolipoprotein binding / clathrin-coated pit / VLDLR internalisation and degradation / cholesterol metabolic process / receptor-mediated endocytosis / memory / calcium-dependent protein binding / symbiont-mediated suppression of host gene expression / nervous system development / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / receptor complex / symbiont entry into host cell / lysosomal membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / calcium ion binding / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / signal transduction / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm
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 / : / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Calcium-binding EGF domain / 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: To Be Published
Title: Structural basis for VLDLR recognition by eastern equine encephalitis virus
Authors: Abraham, J. / Yang, P. / Li, W. / Fan, X. / Pan, J.
History
DepositionSep 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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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

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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

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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