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- PDB-8ihp: Structure of Semliki Forest virus VLP in complex with the recepto... -

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Basic information

Entry
Database: PDB / ID: 8ihp
TitleStructure of Semliki Forest virus VLP in complex with the receptor VLDLR-LA3
Components
  • (Spike glycoprotein ...) x 2
  • Capsid protein
  • Very low-density lipoprotein receptor
KeywordsVIRAL PROTEIN / Semliki Forest virus / SFV / receptor / complex / VLDLR / glycoprotein
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 / reelin-mediated signaling pathway ...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 / reelin-mediated signaling pathway / togavirin / very-low-density lipoprotein particle / cargo receptor activity / T=4 icosahedral viral capsid / positive regulation of dendrite development / dendrite morphogenesis / lipid transport / regulation of synapse assembly / virion assembly / small molecule binding / apolipoprotein binding / clathrin-coated pit / receptor-mediated endocytosis / cholesterol metabolic process / VLDLR internalisation and degradation / 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 / receptor complex / viral translational frameshifting / lysosomal membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / calcium ion binding / 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 / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / : / Calcium-binding EGF domain / 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
Similarity search - Component
Biological speciesSemliki Forest virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsCao, D. / Ma, B. / Cao, Z. / 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: Cell / Year: 2023
Title: Structure of Semliki Forest virus in complex with its receptor VLDLR.
Authors: Duanfang Cao / Bingting Ma / Ziyi Cao / Xinzheng Zhang / Ye Xiang /
Abstract: Semliki Forest virus (SFV) is an alphavirus that uses the very-low-density lipoprotein receptor (VLDLR) as a receptor during infection of its vertebrate hosts and insect vectors. Herein, we used ...Semliki Forest virus (SFV) is an alphavirus that uses the very-low-density lipoprotein receptor (VLDLR) as a receptor during infection of its vertebrate hosts and insect vectors. Herein, we used cryoelectron microscopy to study the structure of SFV in complex with VLDLR. We found that VLDLR binds multiple E1-DIII sites of SFV through its membrane-distal LDLR class A (LA) repeats. Among the LA repeats of the VLDLR, LA3 has the best binding affinity to SFV. The high-resolution structure shows that LA3 binds SFV E1-DIII through a small surface area of 378 Å, with the main interactions at the interface involving salt bridges. Compared with the binding of single LA3s, consecutive LA repeats around LA3 promote synergistic binding to SFV, during which the LAs undergo a rotation, allowing simultaneous key interactions at multiple E1-DIII sites on the virion and enabling the binding of VLDLRs from divergent host species to SFV.
History
DepositionFeb 23, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 24, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)464,69330
Polymers461,91915
Non-polymers2,77515
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein
Spike glycoprotein E2 / E2 envelope glycoprotein


Mass: 46870.277 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
#2: Protein
Spike glycoprotein E1 / E1 envelope glycoprotein


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: P03315

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Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 22 molecules CFILMNO

#3: Protein
Capsid protein / Coat protein / C


Mass: 17848.350 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
#4: Protein/peptide Very low-density lipoprotein receptor / VLDL receptor / VLDL-R


Mass: 4361.682 Da / Num. of mol.: 3
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: 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
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
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / 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: Semliki Forest virus VLP in complex with its receptor VLDLR at the asymmetric unit
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Semliki Forest virus
Source (recombinant)Organism: Homo sapiens (human)
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: 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: 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

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 651086 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00633251
ELECTRON MICROSCOPYf_angle_d0.6745271
ELECTRON MICROSCOPYf_dihedral_angle_d20.3194595
ELECTRON MICROSCOPYf_chiral_restr0.0495056
ELECTRON MICROSCOPYf_plane_restr0.0055846

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