SAXSdb — 11lt

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

Capsid protein VP1

Human enterovirus D68

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Capsid protein VP0 × 1 （A0A5B9NIG2） Capsid protein VP3 × 1 （A0A1L7H9D2） 1E11 Fab heavy chain × 1 1E11 Fab light chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Capsid protein VP1 × 1 （A0A7G9XUH9） Capsid protein VP3 × 1 （A0A1L7H9D2） 1E11 Fab heavy chain × 1 1E11 Fab light chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Capsid protein VP1 × 1 （A0A7G9XUH9） Capsid protein VP0 × 1 （A0A5B9NIG2） 1E11 Fab heavy chain × 1 1E11 Fab light chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

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.

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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

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

11lt__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

11lt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

11lt__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	31.73 Å
Rg (electron density)	30.91 Å
Total Rg	31.69 Å
Atom count	7004
Residues	895
Excluded volume	124270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`11lt__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	Human enterovirus D68
Common name common_name	EV68, EV-68
NCBI taxonomy ID ncbi_taxonomy_id	42789
Host organism 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

Source Source

Source organism organism	Human enterovirus D68
Common name common_name	EV68, EV-68
NCBI taxonomy ID ncbi_taxonomy_id	42789
Host organism 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

Source Source

Source organism organism	Human enterovirus D68
Common name common_name	EV68, EV-68
NCBI taxonomy ID ncbi_taxonomy_id	42789
Host organism 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

Source Source

Source organism organism	Macaca mulatta
Common name common_name	Rhesus monkey
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism 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

Source Source

Source organism organism	Macaca mulatta
Common name common_name	Rhesus monkey
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Homo sapiens

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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Method resolution_method	—
颗粒数 num_particles	724000

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

11lt__assembly_1__model_1

11lt__assembly_1__model_1 | I(q)

11lt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

7. Citations (1)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Capsid protein VP0

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Capsid protein VP3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

11lt__assembly_1__model_1

11lt__assembly_1__model_1 | I(q)

11lt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

7. Citations (1)