SAXSdb — 9c4a

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

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 180	VP0 × 60 （A0A141B2D4） VP3 × 60 （A0A097BW19）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	VP0 × 1 （A0A141B2D4） VP3 × 1 （A0A097BW19）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 15	VP0 × 5 （A0A141B2D4） VP3 × 5 （A0A097BW19）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 18	VP0 × 6 （A0A141B2D4） VP3 × 6 （A0A097BW19）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	VP0 × 1 （A0A141B2D4） VP3 × 1 （A0A097BW19）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8D5ZMD3_HED68
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–296； UniProt 565–860

VP0

Human enterovirus D68

UniProt A0A141B2D4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 180	VP1 × 60 （A0A8D5ZMD3） VP3 × 60 （A0A097BW19）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	VP1 × 1 （A0A8D5ZMD3） VP3 × 1 （A0A097BW19）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 15	VP1 × 5 （A0A8D5ZMD3） VP3 × 5 （A0A097BW19）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 18	VP1 × 6 （A0A8D5ZMD3） VP3 × 6 （A0A097BW19）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	VP1 × 1 （A0A8D5ZMD3） VP3 × 1 （A0A097BW19）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A141B2D4_HED68
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–317； UniProt 1–317

VP3

Human enterovirus D68

UniProt A0A097BW19

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 180	VP1 × 60 （A0A8D5ZMD3） VP0 × 60 （A0A141B2D4）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	VP1 × 1 （A0A8D5ZMD3） VP0 × 1 （A0A141B2D4）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 15	VP1 × 5 （A0A8D5ZMD3） VP0 × 5 （A0A141B2D4）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 18	VP1 × 6 （A0A8D5ZMD3） VP0 × 6 （A0A141B2D4）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 3	VP1 × 1 （A0A8D5ZMD3） VP0 × 1 （A0A141B2D4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A097BW19_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	9c4a
Deposition date deposition_date	2024-06-03
Structure title title	Cryo-EM Structure of EV-D68 Vaccine Candidate - A2 Subclade Virus-like Particle
Keywords keywords	EV-D68, A2 subclade, VLP, 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.

9c4a__assembly_1__model_1

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

Download this curve (.dat)

9c4a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9c4a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	140.10 Å
Total Rg	140.10 Å
Atom count	305040
Residues	38760
Excluded volume	5433500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9c4a__assembly_1__model_1`	180-meric （180）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9c4a__assembly_2__model_1`	trimeric （3）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`9c4a__assembly_3__model_1`	pentadecameric （15）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`9c4a__assembly_4__model_1`	octadecameric （18）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`9c4a__assembly_5__model_1`	trimeric （3）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	VP1
Molecular weight formula_weight	33014.5 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	5084

IESIIKTATDTVKSEINAELGVVPSLNAVETGASSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKNHTSSEARTDKNFYKWTINTKSFVQLRRKLELFTYLRFDAEITILTTVAVGSNNSTYMGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKVSDPPARMTIPFMCINSAYSVFYDGFAGFEKNGLYGINPADTIGNLCVRIVNEHQPIGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGKERAPNALNAIIGNRESVKTMPHDIRLV

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	VP0
Molecular weight formula_weight	35074.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGAQVTRQQTGTHENANIATNGSHITYNQINFYKDSYAASASKQDFSQDPSKFTEPVVEGLKAGAPVLKSPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLKSVKWETESTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTTTSPGFDDIMKGEEGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTVSSMVPITVSIAPMCCEFNGLRHAITQ

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	VP3
Molecular weight formula_weight	27282.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQVRNMLEVIQVESMMEINNTENAVGMQRLKVDISVLTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLVIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSNTCSLIGFVAAKDDFSLRLMRDSPDIGQLEHLHEAEAAYQ

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

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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	2.43 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	37000

Cryo-EM Structure of EV-D68 Vaccine Candidate - A2 Subclade Virus-like Particle

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

VP1

State in the Current Structure

Other States of the Same Protein in the Database

VP0

State in the Current Structure

Other States of the Same Protein in the Database

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

9c4a__assembly_1__model_1

9c4a__assembly_1__model_1 | I(q)

9c4a__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

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

7. Citations (1)

Cryo-EM Structure of EV-D68 Vaccine Candidate - A2 Subclade Virus-like Particle

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

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

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

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

9c4a__assembly_1__model_1

9c4a__assembly_1__model_1 | I(q)

9c4a__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

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

7. Citations (1)