SAXSdb — 11lt

▼

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

Capsid protein VP1

Human enterovirus D68

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 54–282	Not recorded	Capsid protein VP0 × 1 （A0A5B9NIG2） Capsid protein VP3 × 1 （A0A1L7H9D2） 1E11 Fab heavy chain × 1 1E11 Fab light chain × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.63 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 11LT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11OV Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 5H03 Deposited 2026-03-06	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 54–282（229 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å

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

View Construct and Data Evidence

UniProt name	A0A7G9XUH9_HED68
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–229； UniProt 54–282

Capsid protein VP0

Human enterovirus D68

UniProt A0A5B9NIG2

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain B； UniProt 98–309	Not recorded	Capsid protein VP1 × 1 （A0A7G9XUH9） Capsid protein VP3 × 1 （A0A1L7H9D2） 1E11 Fab heavy chain × 1 1E11 Fab light chain × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.63 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 11LT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11OV Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 5H03 Deposited 2026-03-06	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 98–309（212 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å

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

View Construct and Data Evidence

UniProt name	A0A5B9NIG2_HED68
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–212； UniProt 98–309

Capsid protein VP3

Human enterovirus D68

UniProt A0A1L7H9D2

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain C； UniProt 318–564	Not recorded	Capsid protein VP1 × 1 （A0A7G9XUH9） Capsid protein VP0 × 1 （A0A5B9NIG2） 1E11 Fab heavy chain × 1 1E11 Fab light chain × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.63 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 11LT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11OV Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 5H03 Deposited 2026-03-06	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 318–564（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
9C8F Cryo-EM Structure of EV-D68 B3 A-Particle Deposited 2024-06-12	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 180 PDB declaration: 180-meric	Chain C 318–564（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
9C8F Cryo-EM Structure of EV-D68 B3 A-Particle Deposited 2024-06-12	Different oligomeric state Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 318–564（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
9C8F Cryo-EM Structure of EV-D68 B3 A-Particle Deposited 2024-06-12	Different oligomeric state Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain C 318–564（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
9C8F Cryo-EM Structure of EV-D68 B3 A-Particle Deposited 2024-06-12	Different oligomeric state Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain C 318–564（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
9C8F Cryo-EM Structure of EV-D68 B3 A-Particle Deposited 2024-06-12	Different oligomeric state Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 318–564（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
9C8I Cryo-EM Structure of EV-D68 B3 Inactivated Virus Particle Deposited 2024-06-12	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 240 PDB declaration: 240-meric	Chain C 318–564（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å
9C8I Cryo-EM Structure of EV-D68 B3 Inactivated Virus Particle Deposited 2024-06-12	Different oligomeric state Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 318–564（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å
9C8I Cryo-EM Structure of EV-D68 B3 Inactivated Virus Particle Deposited 2024-06-12	Different oligomeric state Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain C 318–564（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å
9C8I Cryo-EM Structure of EV-D68 B3 Inactivated Virus Particle Deposited 2024-06-12	Different oligomeric state Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain C 318–564（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å
9C8I Cryo-EM Structure of EV-D68 B3 Inactivated Virus Particle Deposited 2024-06-12	Different oligomeric state Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 318–564（247 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å

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

View Construct and Data Evidence

UniProt name	A0A1L7H9D2_HED68
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–247； UniProt 318–564

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	11lt
Deposition date deposition_date	2026-03-03
Structure title title	Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 1E11
Keywords keywords	EV-D68, B3 subclade, Virus-like particle vaccine, 1E11 neutralizing antibody, 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	31.73 Å
Radius of gyration Rg (electron density) rg_electron	30.91 Å
Forward intensity I(0) i0	155930000.00
Molecular weight molecular_weight	99402.0 kDa
Excluded volume excluded_volume	124270 Å³
Envelope volume envelope_volume	157120 Å³
Hydration-shell volume shell_volume	41506 Å³
Envelope diameter envelope_diameter	101.0 Å
Shell Rg shell_rg	38.58 Å
Envelope Rg envelope_rg	31.24 Å
Shape Rg shape_rg	30.88 Å
Total Rg total_rg	31.69 Å
Total atoms total_atoms	7004
Residues n_residues	895
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	99.9 Å
Rg (real space) rg_real	31.60 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	1.5590e+08
I(0) uncertainty (real space) i0_real_error	2.2500e+06
Rg (reciprocal space) rg_reciprocal	31.66 Å
I(0) (reciprocal space) i0_reciprocal	155900000.0000
Solution quality estimate total_estimate	0.9067
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.0 Å
Skewness Skewness skewness	0.182
Kurtosis Kurtosis kurtosis	-0.559
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	33840000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.947

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Capsid protein VP1
Molecular weight formula_weight	25735.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7004

VSETLVENFLSRAALVSKRSFEYKDHTSSTAQTDKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSNNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKTGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGKERAPNALNAIIG

来源 Source

来源生物 organism	Human enterovirus D68
通用名 common_name	EV68, EV-68
NCBI Class编号 ncbi_taxonomy_id	42789
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Capsid protein VP0
Molecular weight formula_weight	23797.0 kDa
EC 编号 ec_number	3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLRSVKWEATSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTTTSPGFDDIMKGEAGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTMSSMVPITVSIAPMCCEFN

来源 Source

来源生物 organism	Human enterovirus D68
通用名 common_name	EV68, EV-68
NCBI Class编号 ncbi_taxonomy_id	42789
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Capsid protein VP3
Molecular weight formula_weight	27170.9 kDa
EC 编号 ec_number	3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSITLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQIDHLHGAEAAYQ

来源 Source

来源生物 organism	Human enterovirus D68
通用名 common_name	EV68, EV-68
NCBI Class编号 ncbi_taxonomy_id	42789
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	1E11 Fab heavy chain
Molecular weight formula_weight	13879.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVKLQQWGEGLVKPSETLSLTCAVYGGSIHGYYYWSWIRQPPGKGLEWIGYIYGDNFSTNYNPSLKNRVTISKDTPRNQFSLRLTSVTAADTALYFCAREAGSRNAYNWFDVWGPGVRVAVTS

来源 Source

来源生物 organism	Macaca mulatta
通用名 common_name	Rhesus monkey
NCBI Class编号 ncbi_taxonomy_id	9544
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	1E11 Fab light chain
Molecular weight formula_weight	11805.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

QSALTQPPSVSRSLGQSVTISCTATSSDITFYYGVSWYQHHSGTAPRLLIYEVNERPSGVSNRFSGSKSGNTASLTISGVQADDEADYYCGTYRTGNTWVFGGGTRLTVL

来源 Source

来源生物 organism	Macaca mulatta
通用名 common_name	Rhesus monkey
NCBI Class编号 ncbi_taxonomy_id	9544
宿主生物 host_organism	Homo sapiens

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.630 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.63 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	724000

fit	/app/data/saxs_computation/1l/11lt/11lt.fit
pddf	/app/data/pr_computation/1l/11lt/11lt.pr.out
profile	/app/data/saxs_computation/1l/11lt/11lt.dat

Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 1E11

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

Capsid protein VP0

State in the Current Structure

Other States of the Same Protein in the Database

Capsid protein VP3

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

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 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)