SAXSdb — 8dan

▼

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

E1 envelope glycoprotein

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 798–1235 Chain B； UniProt 321–735 Chain D； UniProt 798–1235 Chain E； UniProt 321–735 Chain G； UniProt 798–1235 Chain H； UniProt 321–735 Chain J； UniProt 798–1235 Chain K； UniProt 321–735	Not recorded	Matrix remodeling-associated protein 8 × 4 （A0A7K7KW08） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.74 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 8DAN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8DAQ CryoEM structure of Western equine encephalitis virus VLP Deposited 2022-06-13	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 798–1235（438 aa） Chain B 321–735（415 aa） Chain C 798–1235（438 aa） Chain D 321–735（415 aa） Chain E 798–1235（438 aa） Chain F 321–735（415 aa） Chain G 798–1235（438 aa） Chain H 321–735（415 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 4.35 Å
8SQN CryoEM structure of Western equine encephalitis virus VLP in complex with the chimeric Du-D1-Mo-D2 MXRA8 receptor Deposited 2023-05-04	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain B 798–1235（438 aa） Fragment：UNP residues 798-1235 Chain D 321–735（415 aa） Fragment：UNP residues 321-735 Chain F 798–1235（438 aa） Fragment：UNP residues 798-1235 Chain H 321–735（415 aa） Fragment：UNP residues 321-735 Chain J 798–1235（438 aa） Fragment：UNP residues 798-1235 Chain L 321–735（415 aa） Fragment：UNP residues 321-735 Chain N 798–1235（438 aa） Fragment：UNP residues 798-1235 Chain P 321–735（415 aa） Fragment：UNP residues 321-735	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.89 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 B 320–722（403 aa） Chain E 320–722（403 aa） Chain H 320–722（403 aa） Chain K 320–722（403 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 798–1234（437 aa） Fragment：UNP residues 798-1235 Chain B 320–725（406 aa） Chain D 798–1234（437 aa） Fragment：UNP residues 798-1235 Chain E 320–725（406 aa） Chain G 798–1234（437 aa） Fragment：UNP residues 798-1235 Chain H 320–725（406 aa） Chain J 798–1234（437 aa） Fragment：UNP residues 798-1235 Chain K 320–725（406 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
9E96 WEEV CBA87 VLP in complex with human PCDH10-EC1 Deposited 2024-11-07	Different construct 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 A 798–1236（439 aa） Chain B 330–737（408 aa） Chain F 798–1236（439 aa） Chain G 330–737（408 aa） Chain J 798–1236（439 aa） Chain K 330–737（408 aa） Chain N 798–1236（439 aa） Chain O 330–737（408 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

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q1W679_WEEV
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–438； UniProt 798–1235 Author chain D； PDBConstruct 1–438； UniProt 798–1235 Author chain G； PDBConstruct 1–438； UniProt 798–1235 Author chain J； PDBConstruct 1–438； UniProt 798–1235 Author chain B； PDBConstruct 1–415； UniProt 321–735 Author chain E； PDBConstruct 1–415； UniProt 321–735 Author chain H； PDBConstruct 1–415； UniProt 321–735 Author chain K； PDBConstruct 1–415； UniProt 321–735

Matrix remodeling-associated protein 8

Asarcornis scutulata

UniProt A0A7K7KW08

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain C； UniProt 31–295 Chain F； UniProt 31–295 Chain I； UniProt 31–295 Chain L； UniProt 31–295	Not recorded	E1 envelope glycoprotein × 4 （Q1W679） E2 envelope glycoprotein × 4 （Q1W679） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.74 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A7K7KW08_9AVES
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–265； UniProt 31–295 Author chain F； PDBConstruct 1–265； UniProt 31–295 Author chain I； PDBConstruct 1–265； UniProt 31–295 Author chain L； PDBConstruct 1–265； UniProt 31–295

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8dan
Deposition date deposition_date	2022-06-13
Structure title title	CryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor
Keywords keywords	;WEEV, MXRA8, Receptor, Alphavirus, Avian, VLP, Structural Genomics, PSI-2, Protein Structure Initiative, Center for Structural Genomics of Infectious Diseases, CSGID, VIRUS LIKE PARTICLE ;; VIRUS LIKE PARTICLE
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	61.09 Å
Radius of gyration Rg (electron density) rg_electron	60.84 Å
Forward intensity I(0) i0	3560670000.00
Molecular weight molecular_weight	497650.0 kDa
Excluded volume excluded_volume	620560 Å³
Envelope volume envelope_volume	1038800 Å³
Hydration-shell volume shell_volume	139130 Å³
Envelope diameter envelope_diameter	214.3 Å
Shell Rg shell_rg	65.43 Å
Envelope Rg envelope_rg	59.61 Å
Shape Rg shape_rg	60.77 Å
Total Rg total_rg	61.18 Å
Total atoms total_atoms	68968
Residues n_residues	4472
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

▼

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

Maximum dimension Dmax dmax	202.9 Å
Rg (real space) rg_real	60.84 Å
Rg uncertainty (real space) rg_real_error	1.45 Å
I(0) (real space) i0_real	3.5610e+09
I(0) uncertainty (real space) i0_real_error	7.2270e+07
Rg (reciprocal space) rg_reciprocal	61.28 Å
I(0) (reciprocal space) i0_reciprocal	3563000000.0000
Solution quality estimate total_estimate	0.8746
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	78.0 Å
Skewness Skewness skewness	0.197
Kurtosis Kurtosis kurtosis	-0.427
Angular range angular_range	— – 0.1300 Å⁻¹
Current regularization parameter α current_alpha	0.0004
Highest regularization parameter α highest_alpha	316200000.0000
Real-space data points n_real_points	27
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.812

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	E1 envelope glycoprotein
Molecular weight formula_weight	47188.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	68968

FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVVPSPQVKCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAVALKVHTAALKVGLRIVYGNTTARLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIRKGLVYNYDFPEYGAMNPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGYEMWKNNSGRPLQETAPFGCKIEVEPLRATNCAYGHIPISIDIPDAAFVRSSESPTILEVSCTVADCIYSADFGGSLTLQYKANREGHCPVHSHSTTAVLKEATTHVTATGSITLHFSTSSPQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSLIVVGLIVLVCSSMLINTR

来源 Source

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

Entity 2 Entity 2 polymer

Description description	E2 envelope glycoprotein
Molecular weight formula_weight	46171.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K

ITDDFTLTSPYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTADVTKFRYMSYDHDHDIKEDSMEKLAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGASENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYLEEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKRDQTKWVFNSPDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKLGLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYYHRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLC

来源 Source

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

Entity 3 Entity 3 polymer

Description description	Matrix remodeling-associated protein 8
Molecular weight formula_weight	30615.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

NSVVVSVLNISATLGSQAVLPCKSYRMVWTQDRLNDRQRVVHWDVYSTYYGDNKMERLCDMYSAGDQRVYSSYNQGRIFMPQNAFTDGNFSLVIKDVAESDGGIYSCNLHHHYCHLYETVKIQLDVTKKAKAAKEYWDGEKAVIVALEGSTVMLPCVNRNQIWTERHSEEEQQVVHWDRQPPGVPHDRADRLIDLYASGERRSYGPLFIRQKMNITDTAFALGDFSLRISELESADEGTYSCHLHHHYCGLHERRIYQVFVTEPV

来源 Source

来源生物 organism	Asarcornis scutulata
NCBI Class编号 ncbi_taxonomy_id	75869
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	12

▶

8. Citations (1)

▶

Resolution resolution	4.74 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	250347

fit	/app/data/saxs_computation/da/8dan/8dan.fit
pddf	/app/data/pr_computation/da/8dan/8dan.pr.out
profile	/app/data/saxs_computation/da/8dan/8dan.dat

CryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor

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

E1 envelope glycoprotein

State in the Current Structure

Other States of the Same Protein in the Database

Matrix remodeling-associated protein 8

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)