SAXSdb — 9l3v

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Structural polyprotein

Western equine encephalitis virus

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 798–1236 Chain C； UniProt 798–1236 Chain E； UniProt 798–1236	Not recorded	Structural polyprotein × 3 （C7EPG2）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 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 9L3V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9L1N Structure of Western equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1 Deposited 2024-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric	Chain A 798–1236（439 aa） Chain B 320–735（416 aa） Chain C 110–259（150 aa） Chain D 798–1236（439 aa） Chain E 320–735（416 aa） Chain F 110–259（150 aa） Chain G 798–1236（439 aa） Chain H 320–735（416 aa） Chain I 110–259（150 aa） Chain J 798–1236（439 aa） Chain K 320–735（416 aa） Chain L 110–259（150 aa）	Not recorded	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
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 oligomeric state 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
Chains and sequence ranges	Author chain A； PDBConstruct 1–439； UniProt 798–1236 Author chain C； PDBConstruct 1–439； UniProt 798–1236 Author chain E； PDBConstruct 1–439； UniProt 798–1236

Structural polyprotein

Western equine encephalitis virus

UniProt C7EPG2

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain B； UniProt 320–737 Chain D； UniProt 320–737 Chain F； UniProt 320–737	Not recorded	Structural polyprotein × 3 （Q9J1K1）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 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 9L3V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain B 320–737（418 aa） Chain D 320–737（418 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 2.99 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C7EPG2_WEEV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–418； UniProt 320–737 Author chain D； PDBConstruct 1–418； UniProt 320–737 Author chain F； PDBConstruct 1–418； UniProt 320–737

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9l3v
Deposition date deposition_date	2024-12-19
最后修订 last_revision	2025-08-27
Structure title title	structure of WEEV strain 71V1658 virus-like particle(3-fold region)
Keywords keywords	WEEV, VLP, E2-E1 glycoproteins, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	53.42 Å
Radius of gyration Rg (electron density) rg_electron	53.10 Å
Forward intensity I(0) i0	1136310000.00
Molecular weight molecular_weight	280850.0 kDa
Excluded volume excluded_volume	351470 Å³
Envelope volume envelope_volume	554830 Å³
Hydration-shell volume shell_volume	87200 Å³
Envelope diameter envelope_diameter	179.7 Å
Shell Rg shell_rg	55.83 Å
Envelope Rg envelope_rg	53.10 Å
Shape Rg shape_rg	53.00 Å
Total Rg total_rg	53.53 Å
Total atoms total_atoms	19743
Residues n_residues	2571
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	176.5 Å
Rg (real space) rg_real	53.29 Å
Rg uncertainty (real space) rg_real_error	1.62 Å
I(0) (real space) i0_real	1.1360e+09
I(0) uncertainty (real space) i0_real_error	2.2330e+07
Rg (reciprocal space) rg_reciprocal	53.51 Å
I(0) (reciprocal space) i0_reciprocal	1137000000.0000
Solution quality estimate total_estimate	0.8827
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	66.9 Å
Skewness Skewness skewness	0.187
Kurtosis Kurtosis kurtosis	-0.435
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	44870000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.859

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Structural polyprotein
Molecular weight formula_weight	47326.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	19743

FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVIPSPQVKCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAVALKVHTAALKVGLRIVYGNTTAHLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIRKGLVYNYDFPEYGAMKPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGYEMWKNNSGRPLQETAPFGCKIEVEPLRASNCAYGHIPISIDIPDAAFVRSSESPTILEVSCTVADCIYSADFGGSLTLQYKADREGHCPVHSHSTTAVLKEATTHVTAVGSITLHFSTSSPQANFIVSLCGKKSTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSLIVVGLIVLVCSSMLINTRR

来源 Source

来源生物 organism	Western equine encephalitis virus
NCBI Class编号 ncbi_taxonomy_id	11039
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Structural polyprotein
Molecular weight formula_weight	46435.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

SITDDFTLTSPYLGFCPYCRHSTPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTADVTKFRYMSFDHDHDIKEDSMEKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGASENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYLEEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKSDQTKWVFNSPDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTAMRPTLLTTRKLGLRADATAEWITGSTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYYHRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLCCI

来源 Source

来源生物 organism	Western equine encephalitis virus
NCBI Class编号 ncbi_taxonomy_id	11039
宿主生物 host_organism	Homo sapiens

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8. Citations (1)

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Resolution resolution	2.530 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.53 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	842545

fit	/app/data/saxs_computation/l3/9l3v/9l3v.fit
pddf	/app/data/pr_computation/l3/9l3v/9l3v.pr.out
profile	/app/data/saxs_computation/l3/9l3v/9l3v.dat

structure of WEEV strain 71V1658 virus-like particle(3-fold region)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Structural polyprotein

State in the Current Structure

Other States of the Same Protein in the Database

Structural polyprotein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)