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9l1n

Structure of Western equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1

Method: ELECTRON MICROSCOPY Dmax: 216.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E1 glycoprotein

Western equine encephalitis virus

UniProt Q9J1K1

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 heterocomplex Heteromer Protein × 13 PDB declaration: 13-meric（13） Consistent with protein copy count Chain A； UniProt 798–1236 Chain B； UniProt 320–735 Chain C； UniProt 110–259 Chain D； UniProt 798–1236 Chain E； UniProt 320–735 Chain F； UniProt 110–259 Chain G； UniProt 798–1236 Chain H； UniProt 320–735 Chain I； UniProt 110–259 Chain J； UniProt 798–1236 Chain K； UniProt 320–735 Chain L； UniProt 110–259 Not recorded Protocadherin-10 × 1 （Q9P2E7） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 9L1N Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9L3V structure of WEEV strain 71V1658 virus-like particle(3-fold region) Deposited 2024-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 798–1236（439 aa）
Chain C 798–1236（439 aa）
Chain E 798–1236（439 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
9L41 Structure of WEEV strain 71V1658 virus-like particles (VLPs) in complex with human PCDH10 extracellular cadherin repeats 1-2 (EC1-EC2)(3-fold region) Deposited 2024-12-19 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 798–1236（439 aa）
Chain C 798–1236（439 aa）
Chain E 798–1236（439 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9J1K1_WEEV
Isoform —
PDB entities 1, 2, 3
Chains and sequence ranges Author chain A； PDBConstruct 1–439； UniProt 798–1236 Author chain D； PDBConstruct 1–439； UniProt 798–1236 Author chain G； PDBConstruct 1–439； UniProt 798–1236 Author chain J； PDBConstruct 1–439； UniProt 798–1236 Author chain B； PDBConstruct 1–416； UniProt 320–735 Author chain E； PDBConstruct 1–416； UniProt 320–735 Author chain H； PDBConstruct 1–416； UniProt 320–735 Author chain K； PDBConstruct 1–416； UniProt 320–735 Author chain C； PDBConstruct 1–150； UniProt 110–259 Author chain F； PDBConstruct 1–150； UniProt 110–259 Author chain I； PDBConstruct 1–150； UniProt 110–259 Author chain L； PDBConstruct 1–150； UniProt 110–259

Protocadherin-10

Homo sapiens

UniProt Q9P2E7

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 heterocomplex Heteromer Protein × 13 PDB declaration: 13-meric（13） Consistent with protein copy count Chain M； UniProt 19–113 Not recorded E1 glycoprotein × 4 （Q9J1K1） E2 glycoprotein × 4 （Q9J1K1） Capsid glycoprotein × 4 （Q9J1K1） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 9L1N Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6VFQ Crystal structure of monomeric human protocadherin 10 EC1-EC4 Deposited 2020-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–455（438 aa）
Not recorded CA CALCIUM ION × 9 MAN alpha-D-mannopyranose × 2 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；296 K；14% PEG 400 (v/v), 0.1M sodium acetate pH 4.6, 0.1M CaCl2, with 30% ethylene glycol (v/v) added as cryoprotectant
Resolution 2.30 Å R-free 0.237
6VFW Crystal structure of human delta protocadherin 10 EC1-EC4 Deposited 2020-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–455（438 aa）
Chain C 18–455（438 aa）
Not recorded CA CALCIUM ION × 18 MAN alpha-D-mannopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；12% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1M Tris-bicine buffer pH8.5, 10% 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine with no further cryoprotection
Resolution 3.60 Å R-free 0.295
6VFW Crystal structure of human delta protocadherin 10 EC1-EC4 Deposited 2020-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 18–455（438 aa）
Chain D 18–455（438 aa）
Not recorded CA CALCIUM ION × 18 MAN alpha-D-mannopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；12% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1M Tris-bicine buffer pH8.5, 10% 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine with no further cryoprotection
Resolution 3.60 Å R-free 0.295
6VFW Crystal structure of human delta protocadherin 10 EC1-EC4 Deposited 2020-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 18–455（438 aa）
Not recorded CA CALCIUM ION × 18 MAN alpha-D-mannopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；12% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1M Tris-bicine buffer pH8.5, 10% 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine with no further cryoprotection
Resolution 3.60 Å R-free 0.295
6VG4 Human protocadherin 10 ectodomain Deposited 2020-01-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–680（663 aa）
Not recorded CA CALCIUM ION × 15 MAN alpha-D-mannopyranose × 3 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；296 K；0.22M CaCl2, 0.1M Na Acetate pH 5.0 with 30% (v/v) glycerol as cryoprotectant and glutaraldehyde (0.5% v/v) added to the reservoir after crystal formation to aid crystal stability by cross-linking
Resolution 3.30 Å R-free 0.284
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain M 19–121（103 aa）
Chain N 19–121（103 aa）
Chain O 19–121（103 aa）
Chain P 19–121（103 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
9E96 WEEV CBA87 VLP in complex with human PCDH10-EC1 Deposited 2024-11-07 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 H 19–122（104 aa）
Chain L 19–122（104 aa）
Chain P 19–122（104 aa）
Chain Q 19–122（104 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
9L41 Structure of WEEV strain 71V1658 virus-like particles (VLPs) in complex with human PCDH10 extracellular cadherin repeats 1-2 (EC1-EC2)(3-fold region) Deposited 2024-12-19 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 R 19–114（96 aa）
Chain S 19–114（96 aa）
Chain T 19–114（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PCD10_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain M； PDBConstruct 1–95； UniProt 19–113

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 9l1n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9l1n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9l1n
Deposition date deposition_date2024-12-15
Structure title titleStructure of Western equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1
Keywords keywordsWestern Equine Encephalitis virus, WEEV, PCDH10, EC1, receptor, complex, glycoprotein, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier66.62 Å
Radius of gyration Rg (electron density) rg_electron65.83 Å
Forward intensity I(0) i02865240000.00
Molecular weight molecular_weight450580.0 kDa
Excluded volume excluded_volume563520 ų
Envelope volume envelope_volume1032300 ų
Hydration-shell volume shell_volume131170 ų
Envelope diameter envelope_diameter206.0 Å
Shell Rg shell_rg68.63 Å
Envelope Rg envelope_rg62.58 Å
Shape Rg shape_rg65.80 Å
Total Rg total_rg66.02 Å
Total atoms total_atoms31688
Residues n_residues4107
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 dmax216.5 Å
Rg (real space) rg_real66.26 Å
Rg uncertainty (real space) rg_real_error1.53 Å
I(0) (real space) i0_real2.8650e+09
I(0) uncertainty (real space) i0_real_error5.5410e+07
Rg (reciprocal space) rg_reciprocal66.87 Å
I(0) (reciprocal space) i0_reciprocal2868000000.0000
Solution quality estimate total_estimate0.8848
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary81.2 Å
Skewness Skewness skewness0.087
Kurtosis Kurtosis kurtosis-0.612
Angular range angular_range— – 0.1200 Å−1
Current regularization parameter α current_alpha0.0006
Highest regularization parameter α highest_alpha128000000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.732
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)