SAXSdb — 9fjd

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

Capsid protein VP1

Coxsackievirus B1

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 × 180 PDB declaration: 180-meric（180） Consistent with protein copy count	Chain 1； UniProt 628–847 Chain 2； UniProt 81–329 Chain 3； UniProt 333–564	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.15 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 9FJD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7X42 Cryo-EM structure of Coxsackievirus B1 pre-A-particle in complex with nAb 8A10 (classified from CVB1 mature virion in complex with 8A10 and 2E6) Deposited 2022-03-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 360 PDB declaration: 360-meric	Chain B 70–332（263 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.88 Å
7X42 Cryo-EM structure of Coxsackievirus B1 pre-A-particle in complex with nAb 8A10 (classified from CVB1 mature virion in complex with 8A10 and 2E6) Deposited 2022-03-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 70–332（263 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.88 Å
7X42 Cryo-EM structure of Coxsackievirus B1 pre-A-particle in complex with nAb 8A10 (classified from CVB1 mature virion in complex with 8A10 and 2E6) Deposited 2022-03-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain B 70–332（263 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.88 Å
7X42 Cryo-EM structure of Coxsackievirus B1 pre-A-particle in complex with nAb 8A10 (classified from CVB1 mature virion in complex with 8A10 and 2E6) Deposited 2022-03-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain B 70–332（263 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.88 Å
7X42 Cryo-EM structure of Coxsackievirus B1 pre-A-particle in complex with nAb 8A10 (classified from CVB1 mature virion in complex with 8A10 and 2E6) Deposited 2022-03-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 70–332（263 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.88 Å
7X4K Cryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (classified from CVB1 mature virion in complex with 8A10 and 9A3) Deposited 2022-03-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-meric	Chain B 70–332（263 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
7X4K Cryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (classified from CVB1 mature virion in complex with 8A10 and 9A3) Deposited 2022-03-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 70–332（263 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
7X4K Cryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (classified from CVB1 mature virion in complex with 8A10 and 9A3) Deposited 2022-03-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	Chain B 70–332（263 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
7X4K Cryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (classified from CVB1 mature virion in complex with 8A10 and 9A3) Deposited 2022-03-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain B 70–332（263 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
7X4K Cryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (classified from CVB1 mature virion in complex with 8A10 and 9A3) Deposited 2022-03-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 70–332（263 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
9FJE Expanded formalin inactivated CVB1 Deposited 2024-05-31	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric	Chain 1 628–847（220 aa） Chain 2 81–329（249 aa） Chain 3 333–564（232 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å

3 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A7T7KAA0_9ENTO
Isoform	—
PDB entities	1, 2, 3
Chains and sequence ranges	Author chain 1； PDBConstruct 1–220； UniProt 628–847 Author chain 2； PDBConstruct 1–249； UniProt 81–329 Author chain 3； PDBConstruct 1–232； UniProt 333–564

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	9fjd
Deposition date deposition_date	2024-05-31
Structure title title	Expanded CVB1-VLP (Tween80)
Keywords keywords	coxsackievirus B1, vaccine, Tween80, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
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	29.54 Å
Radius of gyration Rg (electron density) rg_electron	28.73 Å
Forward intensity I(0) i0	93242600.00
Molecular weight molecular_weight	76341.0 kDa
Excluded volume excluded_volume	95469 Å³
Envelope volume envelope_volume	117850 Å³
Hydration-shell volume shell_volume	34706 Å³
Envelope diameter envelope_diameter	106.8 Å
Shell Rg shell_rg	35.36 Å
Envelope Rg envelope_rg	29.53 Å
Shape Rg shape_rg	28.71 Å
Total Rg total_rg	29.38 Å
Total atoms total_atoms	5365
Residues n_residues	686
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	99.5 Å
Rg (real space) rg_real	29.60 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	9.3240e+07
I(0) uncertainty (real space) i0_real_error	1.4690e+06
Rg (reciprocal space) rg_reciprocal	29.58 Å
I(0) (reciprocal space) i0_reciprocal	93240000.0000
Solution quality estimate total_estimate	0.8702
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.0 Å
Skewness Skewness skewness	0.455
Kurtosis Kurtosis kurtosis	-0.141
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18230000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.837

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Capsid protein VP1
Molecular weight formula_weight	24943.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1
Atom count atom_count	5365

SRSESSIENFLCRAACVYYATYTNNSEKGYAEWVINTRQVAQLRRKLELFTYLRFDLELTFVITSAQQPSTATSVDAPVQTHQIMYVPPGGPVPTKVTDYAWQTSTNPSVFWTEGNAPPRMSIPFISIGNAYSCFYDGWTQFSRNGVYGINTLNNMGTLYMRHVNEAGQGPIKSTVRIYFKPKHVKAWVPRPPRLCQYEKQKNVNFTPTGVTTTRVGITT

来源 Source

来源生物 organism	Coxsackievirus B1
NCBI Class编号 ncbi_taxonomy_id	12071
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Capsid protein VP2
Molecular weight formula_weight	27725.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

RVRSITLGNSTITTQECANVVVGYGVWPEYLKDNEATAEDQPTQPDVATCRFYTLESVQWMKNSAGWWWKLPDALSQMGLFGQNMQYHYLGRTGYTIHVQCNASKFHQGCLLVVCVPEAEMGCSNLNNTPEFAELSGGDTARMFTDTQIGETNSKKVQTAVWNAGMGVGVGNLTIYPHQWINLRTNNSATIVMPYINSVPMDNMFRHNNLTLMIIPFVPLNYSEGSSPYVPITVTIAPMCAEYNGLRLA

来源 Source

来源生物 organism	Coxsackievirus B1
NCBI Class编号 ncbi_taxonomy_id	12071
宿主生物 host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Capsid protein VP3
Molecular weight formula_weight	25486.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3

GLPVMTTPGSTQFLTSDDFQSPSAMPQFDVTPEMQIPGRVNNLMEIAEVDSVVPVNNTEANVNSLKAYQIPVQSNSDNGKQVFGFPLQPGANGVLNRTLLGEILNYYTHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGVPKNRKDAMLGTHVIWDVGLQSSCVLCVPWISQTHYRYVVEDEYTAAGYITCWYQTNIVVPADVQSSCDILCFVSACNDFSVRMLKDTPFIR

来源 Source

来源生物 organism	Coxsackievirus B1
NCBI Class编号 ncbi_taxonomy_id	12071
宿主生物 host_organism	Trichoplusia ni

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8. Citations (1)

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Resolution resolution	2.15 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	117738

fit	/app/data/saxs_computation/fj/9fjd/9fjd.fit
pddf	/app/data/pr_computation/fj/9fjd/9fjd.pr.out
profile	/app/data/saxs_computation/fj/9fjd/9fjd.dat

Expanded CVB1-VLP (Tween80)

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

Capsid protein VP1

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 (3)

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)