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- PDB-8ua8: Structure of Semliki Forest virus VLP in complex with VLDLR LA2 -

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Basic information

Entry
Database: PDB / ID: 8ua8
TitleStructure of Semliki Forest virus VLP in complex with VLDLR LA2
Components
  • (Glycoprotein ...) x 2
  • Assembly protein E3
  • Capsid protein
  • Very low-density lipoprotein receptor
KeywordsVIRUS LIKE PARTICLE / Semliki Forest Virus / Receptor
Function / homology
Function and homology information


reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle binding / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity / togavirin ...reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle binding / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity / togavirin / very-low-density lipoprotein particle clearance / very-low-density lipoprotein particle / T=4 icosahedral viral capsid / positive regulation of dendrite development / dendrite morphogenesis / cargo receptor activity / lipid transport / virion assembly / small molecule binding / apolipoprotein binding / clathrin-coated pit / cholesterol metabolic process / VLDLR internalisation and degradation / receptor-mediated endocytosis / memory / calcium-dependent protein binding / nervous system development / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / receptor complex / viral translational frameshifting / symbiont entry into host cell / lysosomal membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / 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. / Alphavirus E2 glycoprotein, domain B / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / 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. / Alphavirus E2 glycoprotein, domain B / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / 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 E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E3 glycoprotein / 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 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Epidermal growth factor-like 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 / Structural polyprotein / Very low-density lipoprotein receptor
Similarity search - Component
Biological speciesSemliki Forest virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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: Cryo-EM structure of SFV VLP-VLDLRAD2 complex at the 3-fold axes
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: Glycoprotein E1
B: Glycoprotein E2
C: Assembly protein E3
D: Capsid protein
E: Glycoprotein E1
F: Glycoprotein E2
G: Assembly protein E3
H: Capsid protein
I: Glycoprotein E1
J: Glycoprotein E2
K: Assembly protein E3
L: Capsid protein
M: Glycoprotein E1
N: Glycoprotein E2
O: Assembly protein E3
P: Capsid protein
R: Very low-density lipoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)476,83832
Polymers470,28917
Non-polymers6,54815
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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Glycoprotein ... , 2 types, 8 molecules AEIMBFJN

#1: Protein
Glycoprotein E1


Mass: 47489.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Semliki Forest virus / Production host: Homo sapiens (human) / References: UniProt: A0A0F6PP03
#2: Protein
Glycoprotein E2


Mass: 46330.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Semliki Forest virus / Production host: Homo sapiens (human) / References: UniProt: A0A0E3T652

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Protein , 2 types, 8 molecules CGKODHLP

#3: Protein
Assembly protein E3


Mass: 6020.911 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Semliki Forest virus / Production host: Homo sapiens (human) / References: UniProt: P03315
#4: Protein
Capsid protein / Coat protein / C


Mass: 16723.904 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Semliki Forest virus / Production host: Homo sapiens (human) / References: UniProt: P03315, togavirin

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Protein/peptide / Non-polymers , 2 types, 2 molecules R

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


Mass: 4028.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VLDLR / Production host: Homo sapiens (human) / References: UniProt: P98155
#9: 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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Sugars , 3 types, 14 molecules

#6: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 6 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#8: 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.: 2 / 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

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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

ComponentName: Semliki Forest virus / Type: VIRUS / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Semliki Forest virus
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
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: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 439486 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01434078
ELECTRON MICROSCOPYf_angle_d1.35246445
ELECTRON MICROSCOPYf_dihedral_angle_d7.424817
ELECTRON MICROSCOPYf_chiral_restr0.0695266
ELECTRON MICROSCOPYf_plane_restr0.0125972

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