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- PDB-8yw1: Semliki Forest virus viron in complex with VLDLR -

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Basic information

Entry
Database: PDB / ID: 8yw1
TitleSemliki Forest virus viron in complex with VLDLR
Components
  • (Spike glycoprotein ...) x 3
  • Very low-density lipoprotein receptor
  • capsid protein, partial
KeywordsVIRAL PROTEIN / Semliki Forest virus / VLDLR
Function / homology
Function and homology information


reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / ventral spinal cord development / 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 / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / ventral spinal cord development / very-low-density lipoprotein particle binding / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / reelin-mediated signaling pathway / very-low-density lipoprotein particle / positive regulation of dendrite development / cargo receptor activity / 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 / receptor complex / lysosomal membrane / calcium ion binding / glutamatergic synapse / signal transduction / 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 / 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. ...: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / 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. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
: / Very low-density lipoprotein receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Semliki Forest virus 4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsWang, J. / Zheng, T. / Yang, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: PLoS Pathog / Year: 2024
Title: Structural insights into Semiliki forest virus receptor binding modes indicate novel mechanism of virus endocytosis.
Authors: Decheng Yang / Nan Wang / Bingchen Du / Zhenzhao Sun / Shida Wang / Xijun He / Jinyue Wang / Tao Zheng / Yutao Chen / Xiangxi Wang / Jingfei Wang /
Abstract: The Very Low-Density Lipoprotein Receptor (VLDLR) is an entry receptor for the prototypic alphavirus Semliki Forest Virus (SFV). However, the precise mechanisms underlying the entry of SFV into cells ...The Very Low-Density Lipoprotein Receptor (VLDLR) is an entry receptor for the prototypic alphavirus Semliki Forest Virus (SFV). However, the precise mechanisms underlying the entry of SFV into cells mediated by VLDLR remain unclear. In this study, we found that of the eight class A (LA) repeats of the VLDLR, only LA2, LA3, and LA5 specifically bind to the native SFV virion while synergistically promoting SFV cell attachment and entry. Furthermore, the multiple cryo-electron microscopy structures of VLDLR-SFV complexes and mutagenesis studies have demonstrated that under physiological conditions, VLDLR primarily binds to E1-DIII of site-1, site-2, and site-1' at the twofold symmetry axes of SFV virion through LA2, LA3, and LA5, respectively. These findings unveil a novel mechanism for viral entry mediated by receptors, suggesting that conformational transitions in VLDLR induced by multivalent binding of LAs facilitate cellular internalization of SFV, with significant implications for the design of antiviral therapeutics.
History
DepositionMar 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.0Dec 11, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 11, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.1Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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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: Very low-density lipoprotein receptor
D: capsid protein, partial
F: Spike glycoprotein E1
G: Spike glycoprotein E1
H: Spike glycoprotein E1
I: Spike glycoprotein E2
J: Spike glycoprotein E2
K: Spike glycoprotein E2
L: Spike glycoprotein E3
M: Spike glycoprotein E3
N: Spike glycoprotein E3
O: capsid protein, partial
P: capsid protein, partial
Q: capsid protein, partial
S: Spike glycoprotein E3
E: Spike glycoprotein E1
R: Spike glycoprotein E2
T: capsid protein, partial
U: Spike glycoprotein E1
V: Spike glycoprotein E1
W: Spike glycoprotein E1
X: Spike glycoprotein E2
Y: Spike glycoprotein E2
Z: Spike glycoprotein E2
a: Spike glycoprotein E3
b: Spike glycoprotein E3
c: Spike glycoprotein E3
d: capsid protein, partial
e: capsid protein, partial
f: capsid protein, partial
g: Spike glycoprotein E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)967,94257
Polymers953,86533
Non-polymers14,07724
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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Spike glycoprotein ... , 3 types, 24 molecules AFGHEUVWBIJKRXYZLMNSabcg

#1: Protein
Spike glycoprotein E1


Mass: 47489.766 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652
#2: Protein
Spike glycoprotein E2


Mass: 46468.867 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: Molecular name is based on https://www.ebi.ac.uk/interpro/protein/UniProt/A0A0E3T652/ as Uniprot Reference A0A0E3T652 and author provided name are both Structural polyprotein.
Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652
#5: Protein
Spike glycoprotein E3


Mass: 5848.729 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652

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Protein , 2 types, 9 molecules CDOPQTdef

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


Mass: 13075.933 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
#4: Protein
capsid protein, partial


Mass: 17791.299 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652

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Sugars , 1 types, 24 molecules

#6: 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.: 24 / 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

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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 viron in complex with VLDLR-LA3-5
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Semliki Forest virus 4
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44701 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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