SAXSdb — 7ebr

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

Capsid protein 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 360	2H12 Fab heavy chain × 60 2H12 Fab light chain × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	2H12 Fab heavy chain × 1 2H12 Fab light chain × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 30	2H12 Fab heavy chain × 5 2H12 Fab light chain × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 36	2H12 Fab heavy chain × 6 2H12 Fab light chain × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 6	2H12 Fab heavy chain × 1 2H12 Fab light chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A097BW12_HED68
Isoform	—
PDB entities	1, 2, 3, 4
Chains and sequence ranges	Author chain A； PDBConstruct 1–297； UniProt 565–861 Author chain B； PDBConstruct 1–247； UniProt 318–564 Author chain C； PDBConstruct 1–248； UniProt 70–317 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	7ebr
Deposition date deposition_date	2021-03-10
Structure title title	EV-D68 in complex with 2H12 Fab (state S2)
Keywords keywords	Enterovirus D68, Monoclonal antibody, Uncoating, VIRUS; VIRUS
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.

7ebr__assembly_1__model_1

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

Download this curve (.dat)

7ebr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ebr__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)	145.50 Å
Total Rg	145.60 Å
Atom count	453780
Residues	58260
Excluded volume	8069300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ebr__assembly_1__model_1`	360-meric （360）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7ebr__assembly_2__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`7ebr__assembly_3__model_1`	30-meric （30）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`7ebr__assembly_4__model_1`	36-meric （36）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`7ebr__assembly_5__model_1`	hexameric （6）	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	Capsid protein VP1
Molecular weight formula_weight	32920.3 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	7563

IESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKDHTSSTARADKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSGNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARITIPFMCINSAYSVFYDGFAGFEKNGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGKERAPNALSAIIGNRDSVKTMPHNIVNT

Entity 2 Entity 2 polymer

Description description	Capsid protein VP3
Molecular weight formula_weight	27112.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GVPTYLLPGSGQFLTTDDHSSAPALPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMAAGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQLDHLHAAEAAYQ

Entity 3 Entity 3 polymer

Description description	Capsid protein VP2
Molecular weight formula_weight	27567.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLKSVKWETGSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTNTSPGFDDIMKGEEGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTTSSMVPITVSIAPMCCEFNGLRHAITQ

Entity 4 Entity 4 polymer

Description description	Capsid protein 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 polymer

Description description	2H12 Fab heavy chain
Molecular weight formula_weight	22990.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

QVQLQQPGAELVMPGASVKMSCKASGYTFTDYWMHWVKQRPGQGLEWIGAIDTSDSYTTYNRKFKGKATLTVDESSSTAYMQLISLTSEDSAVYYCARGGGGNSPFAYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKI

Entity 6 Entity 6 polymer

Description description	2H12 Fab light chain
Molecular weight formula_weight	23582.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

DIQMTQSPSSLSASLGERVSLTCRASQDIGSSLNWLQQEPDGTIKRLIYATSSLDSGVPKRFSGSRSGSDYSLTISSLESEDFVDYYCLQYASFPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	7ebrC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	7ebrE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7ebrF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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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	3.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1816

EV-D68 in complex with 2H12 Fab (state S2)

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7ebr__assembly_1__model_1

7ebr__assembly_1__model_1 | I(q)

7ebr__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 (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 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

EV-D68 in complex with 2H12 Fab (state S2)

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7ebr__assembly_1__model_1

7ebr__assembly_1__model_1 | I(q)

7ebr__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 (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 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)