SAXSdb — 4wm8

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

VP1

OrganismNot specified

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 （Q68T42） VP3 × 60 （Q68T42） VP4 × 60 （Q8QWD4） DECANOIC ACID × 60 water × 240	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	VP2 × 1 （Q68T42） VP3 × 1 （Q68T42） VP4 × 1 （Q8QWD4） DECANOIC ACID × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 20	VP2 × 5 （Q68T42） VP3 × 5 （Q68T42） VP4 × 5 （Q8QWD4） DECANOIC ACID × 5 water × 20	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 24	VP2 × 6 （Q68T42） VP3 × 6 （Q68T42） VP4 × 6 （Q8QWD4） DECANOIC ACID × 6 water × 24	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	VP2 × 1 （Q68T42） VP3 × 1 （Q68T42） VP4 × 1 （Q8QWD4） DECANOIC ACID × 1 water × 4	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 60	VP2 × 15 （Q68T42） VP3 × 15 （Q68T42） VP4 × 15 （Q8QWD4） DECANOIC ACID × 15 water × 60	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9YLJ3_9ENTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–297； UniProt 13–309

VP2

OrganismNot specified

UniProt Q68T42

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 （Q9YLJ3） VP4 × 60 （Q8QWD4） DECANOIC ACID × 60 water × 240	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （Q9YLJ3） VP4 × 1 （Q8QWD4） DECANOIC ACID × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 20	VP1 × 5 （Q9YLJ3） VP4 × 5 （Q8QWD4） DECANOIC ACID × 5 water × 20	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 24	VP1 × 6 （Q9YLJ3） VP4 × 6 （Q8QWD4） DECANOIC ACID × 6 water × 24	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （Q9YLJ3） VP4 × 1 （Q8QWD4） DECANOIC ACID × 1 water × 4	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 60	VP1 × 15 （Q9YLJ3） VP4 × 15 （Q8QWD4） DECANOIC ACID × 15 water × 60	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q68T42_9ENTO
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain B； PDBConstruct 1–248； UniProt 70–317 Author chain C； PDBConstruct 1–247； UniProt 318–564

VP4

OrganismNot specified

UniProt Q8QWD4

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 （Q9YLJ3） VP2 × 60 （Q68T42） VP3 × 60 （Q68T42） DECANOIC ACID × 60 water × 240	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （Q9YLJ3） VP2 × 1 （Q68T42） VP3 × 1 （Q68T42） DECANOIC ACID × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 20	VP1 × 5 （Q9YLJ3） VP2 × 5 （Q68T42） VP3 × 5 （Q68T42） DECANOIC ACID × 5 water × 20	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 24	VP1 × 6 （Q9YLJ3） VP2 × 6 （Q68T42） VP3 × 6 （Q68T42） DECANOIC ACID × 6 water × 24	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （Q9YLJ3） VP2 × 1 （Q68T42） VP3 × 1 （Q68T42） DECANOIC ACID × 1 water × 4	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 60	VP1 × 15 （Q9YLJ3） VP2 × 15 （Q68T42） VP3 × 15 （Q68T42） DECANOIC ACID × 15 water × 60	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8QWD4_9ENTO
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–68； UniProt 2–69

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	4wm8
Deposition date deposition_date	2014-10-08
Structure title title	Crystal Structure of Human Enterovirus D68
Keywords keywords	Enterovirus, Capsid, Beta jelly roll, Virus; VIRUS
Experimental Method method	X-RAY DIFFRACTION

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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.

4wm8__assembly_1__model_1

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

Download this curve (.dat)

4wm8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4wm8__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)	131.80 Å
Total Rg	131.90 Å
Atom count	377340
Residues	48300
Excluded volume	6711700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4wm8__assembly_1__model_1`	240-meric （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4wm8__assembly_2__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`4wm8__assembly_3__model_1`	eicosameric （20）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`4wm8__assembly_4__model_1`	24-meric （24）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`4wm8__assembly_5__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`4wm8__assembly_6__model_1`	60-meric （60）	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 (6)

Entity 1 Entity 1 polymer

Description description	VP1
Molecular weight formula_weight	32784.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6493

VESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLGRAALVSKKSFEYKNHASSSAGTHKNFFKWTINTKSFVQLRRKLELFTYLRFDAEITILTTVAVNGNNDSTYMGLPDLTLQAMFVPTGALTPKEQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKNGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTMPYMSIANANYKGRDTAPNTLNAIIGNRASVTTMPHNIVTT

Entity 2 Entity 2 polymer

Description description	VP2
Molecular weight formula_weight	27706.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETSTDRFYTLRSVKWESNSTGWWWKLPDALNNIGMFGQNVQYHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHDTTTSPGFNDIMKGERGGTFNHPYVLDDGTSIACATIFPHQWINLRTNNSATIVLPWMNVAPMDFPLRHNQWTLAVIPVVPLGTRTMSSVVPITVSIAPMCCEFNGLRHAITQ

Entity 3 Entity 3 polymer

Description description	VP3
Molecular weight formula_weight	27202.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQIRNMLEMIQVESMMEINNTDGANGMERLRVDISVQADLDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSITLIIPWISGSHYRMFNSDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQSNHLHGAEAAYQ

Entity 4 Entity 4 polymer

Description description	VP4
Molecular weight formula_weight	7337.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GAQVTRQQTGTHENANIATNGSHITYNQINFYKDSYAASASKQDFSQDPSKFTEPVVEGLKAGAPVLK

Entity 5 Entity 5 non-polymer

Description description	DECANOIC ACID
Molecular weight formula_weight	172.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4wm8a_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.0 — automated matches

Domain ID domain_id	d4wm8c_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	4wm8A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4wm8B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4wm8C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	327.000 Å
Unit-cell length b length_b	347.800 Å
Unit-cell length c length_c	357.100 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	120

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	40.250 Å
R factor r_factor	—
R_work r_work	0.2750
R_free r_free	0.2790

Crystal Structure of Human Enterovirus D68

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

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

4wm8__assembly_1__model_1

4wm8__assembly_1__model_1 | I(q)

4wm8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal Structure of Human Enterovirus D68

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

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

4wm8__assembly_1__model_1

4wm8__assembly_1__model_1 | I(q)

4wm8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)