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- PDB-9l1n: Structure of Western equine encephalitis virus 71V1658 strain VLP... -

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Basic information

Entry
Database: PDB / ID: 9l1n
TitleStructure of Western equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1
Components
  • Capsid glycoprotein
  • E1 glycoprotein
  • E2 glycoprotein
  • Protocadherin-10
KeywordsVIRAL PROTEIN / Western Equine Encephalitis virus / WEEV / PCDH10 / EC1 / receptor / complex / glycoprotein
Function / homology
Function and homology information


T=4 icosahedral viral capsid / homophilic cell-cell adhesion / nervous system development / postsynaptic membrane / host cell cytoplasm / cell adhesion / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / calcium ion binding / symbiont entry into host cell ...T=4 icosahedral viral capsid / homophilic cell-cell adhesion / nervous system development / postsynaptic membrane / host cell cytoplasm / cell adhesion / 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 / glutamatergic synapse / virion membrane / structural molecule activity / proteolysis / membrane / plasma membrane
Similarity search - Function
Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin ...Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / 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. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein / Protocadherin-10
Similarity search - Component
Biological speciesWestern equine encephalitis virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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 Rep / Year: 2025
Title: Structural basis for the recognition of two different types of receptors by Western equine encephalitis virus.
Authors: Bingting Ma / Ziyi Cao / Weijia Ding / Xinzheng Zhang / Ye Xiang / Duanfang Cao /
Abstract: Western equine encephalitis virus (WEEV) enters cells via various receptors. Here, we report the cryoelectron microscopy (cryo-EM) structures of WEEV in complex with its receptors PCDH10 and very-low- ...Western equine encephalitis virus (WEEV) enters cells via various receptors. Here, we report the cryoelectron microscopy (cryo-EM) structures of WEEV in complex with its receptors PCDH10 and very-low-density lipoprotein receptor (VLDLR). Structural analysis shows that PCDH10 binds in the cleft formed by adjacent E2-E1 heterodimers of WEEV through its EC1 ectodomain. Residues of viral envelope proteins involved in the interactions with PCDH10 EC1 are unique to WEEV. The strain-specific receptor VLDLR binds WEEV strain McMillan through two consecutive ecto-LDLR class A (LA) repeats. LA1-2, LA2-3, LA3-4, LA4-5, and LA5-6 of VLDLR all have detectable interactions with WEEV. Detailed structures of WEEV in complex with LA1-2 and LA2-3 show that the N-terminal LA repeat binds in the cleft and that the C-terminal LA repeat is attached to the E2 B domain. The acquisition of a single E2 mutation (V265F) allows WEEV strain 71V-1658, originally unable to bind VLDLR, to gain this receptor-binding ability. The binding of VLDLR to WEEV is in a mode different from those of other alphaviruses.
History
DepositionDec 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Jun 4, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E1 glycoprotein
B: E2 glycoprotein
C: Capsid glycoprotein
D: E1 glycoprotein
E: E2 glycoprotein
F: Capsid glycoprotein
G: E1 glycoprotein
H: E2 glycoprotein
I: Capsid glycoprotein
J: E1 glycoprotein
K: E2 glycoprotein
L: Capsid glycoprotein
M: Protocadherin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)452,45621
Polymers450,68613
Non-polymers1,7708
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
E1 glycoprotein / p130


Mass: 47326.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Strain: 71V1658 / Production host: Homo sapiens (human) / References: UniProt: Q9J1K1
#2: Protein
E2 glycoprotein / p130


Mass: 46218.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Strain: 71V1658 / Production host: Homo sapiens (human) / References: UniProt: Q9J1K1
#3: Protein
Capsid glycoprotein / p130


Mass: 16409.549 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Strain: 71V1658 / Production host: Homo sapiens (human) / References: UniProt: Q9J1K1
#4: Protein Protocadherin-10


Mass: 10866.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH10, KIAA1400 / Production host: Homo sapiens (human) / References: UniProt: Q9P2E7
#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.: 8 / 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
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: Western equine encephalitis virus strain 71V1658 VLP in complex with its receptor PCDH10 EC1 at the asymmetric unit
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Western equine encephalitis virus / Strain: strian 71V1658
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: TFS 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

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 516874 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00732573
ELECTRON MICROSCOPYf_angle_d1.0444404
ELECTRON MICROSCOPYf_dihedral_angle_d6.04219310
ELECTRON MICROSCOPYf_chiral_restr0.0665000
ELECTRON MICROSCOPYf_plane_restr0.0095683

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