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8dec

Cryo-EM Structure of Western Equine Encephalitis Virus

Method: ELECTRON MICROSCOPY Dmax: 221.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike glycoprotein E1

Western equine encephalitis virus

UniProt P13897

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 720 PDB declaration: 720-meric（720） Consistent with protein copy count Chain A； UniProt 798–1236 Chain B； UniProt 320–737 Chain E； UniProt 1–259 Chain F； UniProt 798–1236 Chain G； UniProt 320–737 Chain I； UniProt 1–259 Chain J； UniProt 798–1236 Chain K； UniProt 320–737 Chain M； UniProt 1–259 Chain N； UniProt 798–1236 Chain O； UniProt 320–737 Chain R； UniProt 1–259 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.70 Å
2 Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain A； UniProt 798–1236 Chain B； UniProt 320–737 Chain E； UniProt 1–259 Chain F； UniProt 798–1236 Chain G； UniProt 320–737 Chain I； UniProt 1–259 Chain J； UniProt 798–1236 Chain K； UniProt 320–737 Chain M； UniProt 1–259 Chain N； UniProt 798–1236 Chain O； UniProt 320–737 Chain R； UniProt 1–259 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.70 Å
3 Protein homooligomer Homooligomer Protein × 60 PDB declaration: 60-meric（60） Consistent with protein copy count Chain A； UniProt 798–1236 Chain B； UniProt 320–737 Chain E； UniProt 1–259 Chain F； UniProt 798–1236 Chain G； UniProt 320–737 Chain I； UniProt 1–259 Chain J； UniProt 798–1236 Chain K； UniProt 320–737 Chain M； UniProt 1–259 Chain N； UniProt 798–1236 Chain O； UniProt 320–737 Chain R； UniProt 1–259 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.70 Å
4 Protein homooligomer Homooligomer Protein × 72 PDB declaration: 72-meric（72） Consistent with protein copy count Chain A； UniProt 798–1236 Chain B； UniProt 320–737 Chain E； UniProt 1–259 Chain F； UniProt 798–1236 Chain G； UniProt 320–737 Chain I； UniProt 1–259 Chain J； UniProt 798–1236 Chain K； UniProt 320–737 Chain M； UniProt 1–259 Chain N； UniProt 798–1236 Chain O； UniProt 320–737 Chain R； UniProt 1–259 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.70 Å
5 Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain A； UniProt 798–1236 Chain B； UniProt 320–737 Chain E； UniProt 1–259 Chain F； UniProt 798–1236 Chain G； UniProt 320–737 Chain I； UniProt 1–259 Chain J； UniProt 798–1236 Chain K； UniProt 320–737 Chain M； UniProt 1–259 Chain N； UniProt 798–1236 Chain O； UniProt 320–737 Chain R； UniProt 1–259 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8DEC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8DED Cryo-EM Structure of Western Equine Encephalitis Virus VLP in complex with SKW19 fab Deposited 2022-06-20 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 798–1236（439 aa）
Chain B 320–737（418 aa）
Chain F 798–1236（439 aa）
Chain G 320–737（418 aa）
Chain J 798–1236（439 aa）
Chain K 320–737（418 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8DEE Asymmetric Unit of Western Equine Encephalitis Virus Deposited 2022-06-20 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric
Chain A 798–1236（439 aa）
Chain B 320–737（418 aa）
Chain E 1–259（259 aa）
Chain F 798–1236（439 aa）
Chain G 320–737（418 aa）
Chain I 1–259（259 aa）
Chain J 798–1236（439 aa）
Chain K 320–737（418 aa）
Chain M 1–259（259 aa）
Chain N 798–1236（439 aa）
Chain O 320–737（418 aa）
Chain R 1–259（259 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8DEF Cryo-EM Structure of Western Equine Encephalitis Virus VLP in complex with SKW24 fab Deposited 2022-06-20 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 798–1236（439 aa）
Chain B 320–737（418 aa）
Chain F 798–1236（439 aa）
Chain G 320–737（418 aa）
Chain J 798–1236（439 aa）
Chain K 320–737（418 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8DUL Cryo-EM Structure of Antibody SKT05 in complex with Western Equine Encephalitis Virus spike (local refinement from VLP particles) Deposited 2022-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain A 738–1226（489 aa）
Chain B 330–737（408 aa）
Chain F 738–1226（489 aa）
Chain G 330–737（408 aa）
Chain J 738–1226（489 aa）
Chain K 330–737（408 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.17 Å
8DUN Cryo-EM Structure of Antibody SKW11 in complex with Western Equine Encephalitis Virus spike (local refinement from VLP particles) Deposited 2022-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 738–1226（489 aa）
Chain B 330–737（408 aa）
Chain F 738–1226（489 aa）
Chain G 330–737（408 aa）
Chain J 738–1226（489 aa）
Chain K 330–737（408 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.84 Å
9DQV Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1 Deposited 2024-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain C 97–259（163 aa）
Chain F 97–259（163 aa）
Chain I 97–259（163 aa）
Chain L 97–259（163 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DQX Structure of western equine encephalitis virus CBA87 VLP Deposited 2024-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain C 97–259（163 aa）
Chain F 97–259（163 aa）
Chain I 97–259（163 aa）
Chain L 97–259（163 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9DQY Structure of western equine encephalitis virus Imperial 181 VLP in complex with house sparrow PCDH10 EC1 Deposited 2024-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 798–1231（434 aa）
Chain C 798–1231（434 aa）
Chain E 798–1231（434 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9DQZ Structure of western equine encephalitis virus McMillan VLP in complex with human VLDLR Deposited 2024-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain C 102–259（158 aa）
Chain F 102–259（158 aa）
Chain I 102–259（158 aa）
Chain L 102–259（158 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 CA CALCIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9E96 WEEV CBA87 VLP in complex with human PCDH10-EC1 Deposited 2024-11-07 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain E 107–259（153 aa）
Chain I 107–259（153 aa）
Chain M 107–259（153 aa）
Chain R 107–259（153 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
9E9Y WEEV McMillan VLP in complex with VLDLR LA(1-2) Deposited 2024-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain A 798–1236（439 aa）
Chain C 798–1236（439 aa）
Chain E 107–259（153 aa）
Chain F 107–259（153 aa）
Chain G 798–1236（439 aa）
Chain I 107–259（153 aa）
Chain J 798–1236（439 aa）
Chain L 107–259（153 aa）
Not recorded CA CALCIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
9E9Z SINV-WEEV Fleming in complex with VLDLR LA(1-2) Deposited 2024-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain E 107–259（153 aa）
Chain F 107–259（153 aa）
Chain I 107–259（153 aa）
Chain L 107–259（153 aa）
Not recorded CA CALCIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
9L99 Structure of Western equine encephalitis virus McMillan strain in complex with VLDLR LA1-2 Deposited 2024-12-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 798–1208（411 aa）
Chain B 321–689（369 aa）
Chain G 798–1208（411 aa）
Chain H 321–689（369 aa）
Not recorded CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9L9A Structure of Western equine encephalitis virus McMillan strain in complex with VLDLR LA2-3 Deposited 2024-12-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 798–1208（411 aa）
Chain B 321–689（369 aa）
Chain G 798–1208（411 aa）
Chain H 321–689（369 aa）
Not recorded CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9UIH CryoEM structure of Western equine encephalitis virus California VLP Deposited 2025-04-15 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 798–1236（439 aa）
Chain B 320–737（418 aa）
Chain C 798–1236（439 aa）
Chain D 320–737（418 aa）
Chain E 798–1236（439 aa）
Chain F 320–737（418 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9UIO CryoEM structure of Western equine encephalitis virus California VLP in complex with VLDLR-LA1-3 Deposited 2025-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 798–1236（439 aa）
Chain B 320–737（418 aa）
Chain C 798–1236（439 aa）
Chain D 320–737（418 aa）
Chain E 798–1236（439 aa）
Chain F 320–737（418 aa）
Not recorded CA CALCIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9WSL CryoEM structure of Western equine encephalitis virus California VLP in complex with VLDLR-LBD Deposited 2025-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 798–1236（439 aa）
Chain B 320–737（418 aa）
Chain C 798–1236（439 aa）
Chain D 320–737（418 aa）
Chain E 798–1236（439 aa）
Chain F 320–737（418 aa）
Not recorded CA CALCIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLS_WEEV
Isoform —
PDB entities 1, 2, 3
Chains and sequence ranges Author chain A； PDBConstruct 1–439； UniProt 798–1236 Author chain F； PDBConstruct 1–439； UniProt 798–1236 Author chain J； PDBConstruct 1–439； UniProt 798–1236 Author chain N； PDBConstruct 1–439； UniProt 798–1236 Author chain B； PDBConstruct 1–418； UniProt 320–737 Author chain G； PDBConstruct 1–418； UniProt 320–737 Author chain K； PDBConstruct 1–418； UniProt 320–737 Author chain O； PDBConstruct 1–418； UniProt 320–737 Author chain E； PDBConstruct 1–259； UniProt 1–259 Author chain I； PDBConstruct 1–259； UniProt 1–259 Author chain M； PDBConstruct 1–259； UniProt 1–259 Author chain R； PDBConstruct 1–259； UniProt 1–259

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8dec

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8dec
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8dec
Deposition date deposition_date2022-06-20
Structure title titleCryo-EM Structure of Western Equine Encephalitis Virus
Keywords keywordsWestern Equine Encephalitis Virus, Virus-Like Particle, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier65.67 Å
Radius of gyration Rg (electron density) rg_electron64.83 Å
Forward intensity I(0) i02702490000.00
Molecular weight molecular_weight436780.0 kDa
Excluded volume excluded_volume546020 ų
Envelope volume envelope_volume964930 ų
Hydration-shell volume shell_volume124950 ų
Envelope diameter envelope_diameter204.7 Å
Shell Rg shell_rg67.48 Å
Envelope Rg envelope_rg61.33 Å
Shape Rg shape_rg64.79 Å
Total Rg total_rg65.01 Å
Total atoms total_atoms30716
Residues n_residues4000
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax221.0 Å
Rg (real space) rg_real65.30 Å
Rg uncertainty (real space) rg_real_error1.85 Å
I(0) (real space) i0_real2.7030e+09
I(0) uncertainty (real space) i0_real_error5.5390e+07
Rg (reciprocal space) rg_reciprocal65.94 Å
I(0) (reciprocal space) i0_reciprocal2705000000.0000
Solution quality estimate total_estimate0.8897
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary82.9 Å
Skewness Skewness skewness0.062
Kurtosis Kurtosis kurtosis-0.603
Angular range angular_range— – 0.1200 Å−1
Current regularization parameter α current_alpha0.0013
Highest regularization parameter α highest_alpha112400000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.934
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)