SAXSdb — 9c8i

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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 240	VP2 × 60 （A0A6B7FIF3） VP3 × 60 （A0A1L7H9D2） VP4 × 60 （A0A4P8L6Q8）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	VP2 × 1 （A0A6B7FIF3） VP3 × 1 （A0A1L7H9D2） VP4 × 1 （A0A4P8L6Q8）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 20	VP2 × 5 （A0A6B7FIF3） VP3 × 5 （A0A1L7H9D2） VP4 × 5 （A0A4P8L6Q8）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 24	VP2 × 6 （A0A6B7FIF3） VP3 × 6 （A0A1L7H9D2） VP4 × 6 （A0A4P8L6Q8）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	VP2 × 1 （A0A6B7FIF3） VP3 × 1 （A0A1L7H9D2） VP4 × 1 （A0A4P8L6Q8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A5B9NJ24_HED68
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–295； UniProt 565–859

VP2

Human enterovirus D68

UniProt A0A6B7FIF3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 240	VP1 × 60 （A0A5B9NJ24） VP3 × 60 （A0A1L7H9D2） VP4 × 60 （A0A4P8L6Q8）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （A0A5B9NJ24） VP3 × 1 （A0A1L7H9D2） VP4 × 1 （A0A4P8L6Q8）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 20	VP1 × 5 （A0A5B9NJ24） VP3 × 5 （A0A1L7H9D2） VP4 × 5 （A0A4P8L6Q8）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 24	VP1 × 6 （A0A5B9NJ24） VP3 × 6 （A0A1L7H9D2） VP4 × 6 （A0A4P8L6Q8）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （A0A5B9NJ24） VP3 × 1 （A0A1L7H9D2） VP4 × 1 （A0A4P8L6Q8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6B7FIF3_HED68
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–248； UniProt 70–317

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 240	VP1 × 60 （A0A5B9NJ24） VP2 × 60 （A0A6B7FIF3） VP4 × 60 （A0A4P8L6Q8）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （A0A5B9NJ24） VP2 × 1 （A0A6B7FIF3） VP4 × 1 （A0A4P8L6Q8）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 20	VP1 × 5 （A0A5B9NJ24） VP2 × 5 （A0A6B7FIF3） VP4 × 5 （A0A4P8L6Q8）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 24	VP1 × 6 （A0A5B9NJ24） VP2 × 6 （A0A6B7FIF3） VP4 × 6 （A0A4P8L6Q8）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （A0A5B9NJ24） VP2 × 1 （A0A6B7FIF3） VP4 × 1 （A0A4P8L6Q8）	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

VP4

Human enterovirus D68

UniProt A0A4P8L6Q8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 240	VP1 × 60 （A0A5B9NJ24） VP2 × 60 （A0A6B7FIF3） VP3 × 60 （A0A1L7H9D2）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （A0A5B9NJ24） VP2 × 1 （A0A6B7FIF3） VP3 × 1 （A0A1L7H9D2）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 20	VP1 × 5 （A0A5B9NJ24） VP2 × 5 （A0A6B7FIF3） VP3 × 5 （A0A1L7H9D2）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 24	VP1 × 6 （A0A5B9NJ24） VP2 × 6 （A0A6B7FIF3） VP3 × 6 （A0A1L7H9D2）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （A0A5B9NJ24） VP2 × 1 （A0A6B7FIF3） VP3 × 1 （A0A1L7H9D2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A4P8L6Q8_HED68
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–69； UniProt 1–69

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	9c8i
Deposition date deposition_date	2024-06-12
Structure title title	Cryo-EM Structure of EV-D68 B3 Inactivated Virus Particle
Keywords keywords	EV-D68, B3 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.

9c8i__assembly_1__model_1

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

Download this curve (.dat)

9c8i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9c8i__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)	126.50 Å
Total Rg	126.50 Å
Atom count	378720
Residues	48540
Excluded volume	6727400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9c8i__assembly_1__model_1`	240-meric （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9c8i__assembly_2__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`9c8i__assembly_3__model_1`	eicosameric （20）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`9c8i__assembly_4__model_1`	24-meric （24）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`9c8i__assembly_5__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	VP1
Molecular weight formula_weight	32795.2 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	6312

IESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKDHTSSTAQTDKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSNNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKTGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGKERAPNALNAIIGNRDSVKTMPHNIV

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	VP2
Molecular weight formula_weight	27568.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLRSVKWEATSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTTTSPGFDDIMKGEAGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTMSSMVPITVSIAPMCCEFNGLRHAITQ

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	27170.9 kDa
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	VP4
Molecular weight formula_weight	7454.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGAQVTRQQTGTHENANVATNGSHITYNQINFYKDSYAASASKQDFSQDPSKFTEPVVEGLKAGAPVLK

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	2.73 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1700

Cryo-EM Structure of EV-D68 B3 Inactivated Virus 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

VP2

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

VP4

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

9c8i__assembly_1__model_1

9c8i__assembly_1__model_1 | I(q)

9c8i__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 (4)

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

7. Citations (1)

Cryo-EM Structure of EV-D68 B3 Inactivated Virus 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

VP2

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

VP4

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

9c8i__assembly_1__model_1

9c8i__assembly_1__model_1 | I(q)

9c8i__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 (4)

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

7. Citations (1)