7x3c

Cryo-EM structure of Coxsackievirus B1 muture virion in complex with nAbs 8A10 and 5F5 (CVB1-M:8A10:5F5)

Method: ELECTRON MICROSCOPY

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

Virion protein 1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 480	8A10 light chain × 60 8A10 heavy chain × 60 VP2 × 60 （A0A2S0RQC2） VP3 × 60 （L7UV52） Capsid protein VP4 × 60 （A0A2S1FMR1） 5F5 light chain × 60 5F5 heavy chain × 60 PALMITIC ACID × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	8A10 light chain × 1 8A10 heavy chain × 1 VP2 × 1 （A0A2S0RQC2） VP3 × 1 （L7UV52） Capsid protein VP4 × 1 （A0A2S1FMR1） 5F5 light chain × 1 5F5 heavy chain × 1 PALMITIC ACID × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 40	8A10 light chain × 5 8A10 heavy chain × 5 VP2 × 5 （A0A2S0RQC2） VP3 × 5 （L7UV52） Capsid protein VP4 × 5 （A0A2S1FMR1） 5F5 light chain × 5 5F5 heavy chain × 5 PALMITIC ACID × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 48	8A10 light chain × 6 8A10 heavy chain × 6 VP2 × 6 （A0A2S0RQC2） VP3 × 6 （L7UV52） Capsid protein VP4 × 6 （A0A2S1FMR1） 5F5 light chain × 6 5F5 heavy chain × 6 PALMITIC ACID × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 8	8A10 light chain × 1 8A10 heavy chain × 1 VP2 × 1 （A0A2S0RQC2） VP3 × 1 （L7UV52） Capsid protein VP4 × 1 （A0A2S1FMR1） 5F5 light chain × 1 5F5 heavy chain × 1 PALMITIC ACID × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	W8GTF7_9ENTO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–278； UniProt 1–278

VP2

OrganismNot specified

UniProt A0A2S0RQC2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 480	8A10 light chain × 60 8A10 heavy chain × 60 Virion protein 1 × 60 （W8GTF7） VP3 × 60 （L7UV52） Capsid protein VP4 × 60 （A0A2S1FMR1） 5F5 light chain × 60 5F5 heavy chain × 60 PALMITIC ACID × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	8A10 light chain × 1 8A10 heavy chain × 1 Virion protein 1 × 1 （W8GTF7） VP3 × 1 （L7UV52） Capsid protein VP4 × 1 （A0A2S1FMR1） 5F5 light chain × 1 5F5 heavy chain × 1 PALMITIC ACID × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 40	8A10 light chain × 5 8A10 heavy chain × 5 Virion protein 1 × 5 （W8GTF7） VP3 × 5 （L7UV52） Capsid protein VP4 × 5 （A0A2S1FMR1） 5F5 light chain × 5 5F5 heavy chain × 5 PALMITIC ACID × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 48	8A10 light chain × 6 8A10 heavy chain × 6 Virion protein 1 × 6 （W8GTF7） VP3 × 6 （L7UV52） Capsid protein VP4 × 6 （A0A2S1FMR1） 5F5 light chain × 6 5F5 heavy chain × 6 PALMITIC ACID × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 8	8A10 light chain × 1 8A10 heavy chain × 1 Virion protein 1 × 1 （W8GTF7） VP3 × 1 （L7UV52） Capsid protein VP4 × 1 （A0A2S1FMR1） 5F5 light chain × 1 5F5 heavy chain × 1 PALMITIC ACID × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2S0RQC2_9ENTO
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–263； UniProt 70–332

VP3

OrganismNot specified

UniProt L7UV52

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 480	8A10 light chain × 60 8A10 heavy chain × 60 Virion protein 1 × 60 （W8GTF7） VP2 × 60 （A0A2S0RQC2） Capsid protein VP4 × 60 （A0A2S1FMR1） 5F5 light chain × 60 5F5 heavy chain × 60 PALMITIC ACID × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	8A10 light chain × 1 8A10 heavy chain × 1 Virion protein 1 × 1 （W8GTF7） VP2 × 1 （A0A2S0RQC2） Capsid protein VP4 × 1 （A0A2S1FMR1） 5F5 light chain × 1 5F5 heavy chain × 1 PALMITIC ACID × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 40	8A10 light chain × 5 8A10 heavy chain × 5 Virion protein 1 × 5 （W8GTF7） VP2 × 5 （A0A2S0RQC2） Capsid protein VP4 × 5 （A0A2S1FMR1） 5F5 light chain × 5 5F5 heavy chain × 5 PALMITIC ACID × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 48	8A10 light chain × 6 8A10 heavy chain × 6 Virion protein 1 × 6 （W8GTF7） VP2 × 6 （A0A2S0RQC2） Capsid protein VP4 × 6 （A0A2S1FMR1） 5F5 light chain × 6 5F5 heavy chain × 6 PALMITIC ACID × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 8	8A10 light chain × 1 8A10 heavy chain × 1 Virion protein 1 × 1 （W8GTF7） VP2 × 1 （A0A2S0RQC2） Capsid protein VP4 × 1 （A0A2S1FMR1） 5F5 light chain × 1 5F5 heavy chain × 1 PALMITIC ACID × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	L7UV52_9ENTO
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain C； PDBConstruct 1–238； UniProt 333–570

Capsid protein VP4

OrganismNot specified

UniProt A0A2S1FMR1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 480	8A10 light chain × 60 8A10 heavy chain × 60 Virion protein 1 × 60 （W8GTF7） VP2 × 60 （A0A2S0RQC2） VP3 × 60 （L7UV52） 5F5 light chain × 60 5F5 heavy chain × 60 PALMITIC ACID × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	8A10 light chain × 1 8A10 heavy chain × 1 Virion protein 1 × 1 （W8GTF7） VP2 × 1 （A0A2S0RQC2） VP3 × 1 （L7UV52） 5F5 light chain × 1 5F5 heavy chain × 1 PALMITIC ACID × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 40	8A10 light chain × 5 8A10 heavy chain × 5 Virion protein 1 × 5 （W8GTF7） VP2 × 5 （A0A2S0RQC2） VP3 × 5 （L7UV52） 5F5 light chain × 5 5F5 heavy chain × 5 PALMITIC ACID × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 48	8A10 light chain × 6 8A10 heavy chain × 6 Virion protein 1 × 6 （W8GTF7） VP2 × 6 （A0A2S0RQC2） VP3 × 6 （L7UV52） 5F5 light chain × 6 5F5 heavy chain × 6 PALMITIC ACID × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 8	8A10 light chain × 1 8A10 heavy chain × 1 Virion protein 1 × 1 （W8GTF7） VP2 × 1 （A0A2S0RQC2） VP3 × 1 （L7UV52） 5F5 light chain × 1 5F5 heavy chain × 1 PALMITIC ACID × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2S1FMR1_9ENTO
Isoform	—
PDB entities	6
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	7x3c
Deposition date deposition_date	2022-02-28
Structure title title	Cryo-EM structure of Coxsackievirus B1 muture virion in complex with nAbs 8A10 and 5F5 (CVB1-M:8A10:5F5)
Keywords keywords	Coxsackievirus B1, Neutralizing antibody, Cryo-EM, 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.

7x3c__assembly_1__model_1

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

Download this curve (.dat)

7x3c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7x3c__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)	146.80 Å
Total Rg	146.80 Å
Atom count	593400
Residues	76080
Excluded volume	10500000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7x3c__assembly_1__model_1`	480-meric （480）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7x3c__assembly_2__model_1`	octameric （8）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`7x3c__assembly_3__model_1`	40-meric （40）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`7x3c__assembly_4__model_1`	48-meric （48）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`7x3c__assembly_5__model_1`	octameric （8）	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 (9)

Entity 1 Entity 1 polymer

Description description	8A10 light chain
Molecular weight formula_weight	11945.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	9890

DIQMTQTKSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGSVKLLIYYTSTLHSGVPSRFSGSGSGTDYSLTINSLEQEDIATYFCQQGNTFPFTFGGGTKLEIRR

Entity 2 Entity 2 polymer

Description description	8A10 heavy chain
Molecular weight formula_weight	13323.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQQSAAELARPGASVKMSCKASGYTFTTYTMHWVKQRPGQGLEWIGYINPSSRYTEYNQKFKDKTTLTADKSSSTAYMQLSSLTFEDSAVYYCARRSEADRFVYWGQGTLVTVSA

Entity 3 Entity 3 polymer

Description description	Virion protein 1
Molecular weight formula_weight	31207.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

GPVEESVDRAVARVADTISSRPTNSESIPALTAAETGHTSQVVPSDTMQTRHVKNYHSRSESSIENFLCRSACVYYATYTNNSKKGFAEWVINTRQVAQLRRKLELFTYLRFDLELTFVITSAQQPSTASSVDAPVQTHQIMYVPPGGPVPTKVKDYAWQTSTNPSVFWTEGNAPPRMSIPFISIGNAYSCFYDGWTQFSRNGVYGINTLNNMGTLYMRHVNEAGQGPIKSTVRIYFKPKHVKAWVPRPPRLCQYEKQKNVNFSPIGVTTSRTDIITT

Entity 4 Entity 4 polymer

Description description	VP2
Molecular weight formula_weight	29122.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SPSAEECGYSDRVRSITLGNSTITTQECANVVVGYGVWPEYLKDNEATAEDQPTQPDVATCRFYTLESVQWMKNSAGWWWKLPDALSQMGLFGQNMQYHYLGRTGYTIHVQCNASKFHQGCLLVVCVPEAEMGCSNLNNTPEFSELSGGDSARMFTDTQVGESNAKKVQTAVWNAGMGVGVGNLTIFPHQWINLRTNNSATLVMPYINSVPMDNMFRHNNLTLMIIPFVPLNYSEGSSPYVPITVTIAPMCAEYNGLRLASNQ

Entity 5 Entity 5 polymer

Description description	VP3
Molecular weight formula_weight	26328.8 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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GLPVMTTPGSTQFLTSDDFQSPSAMPQFDVTPEMQIPGRVNNLMEIAEVDSVVPVNNTEDNVSSLKAYQIPVQSNSDNGKQVFGFPLQPGANNVLNRTLLGEILNYYTHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGVPKNRKDAMLGTHVIWDVGLQSSCVLCVPWISQTHYRYVVEDEYTAAGYVTCWYQTNIVVPADVQSSCDILCFVSACNDFSVRMLKDTPFIRQDTFYQ

Entity 6 Entity 6 polymer

Description description	Capsid protein VP4
Molecular weight formula_weight	7484.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGAQVSTQKTGAHETGLNASGNSVIHYTNINYYKDAASNSANRQDFTQDPGKFTEPVKDIMVKTMPALN

Entity 7 Entity 7 polymer

Description description	5F5 light chain
Molecular weight formula_weight	11218.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

QIVLSQSPAILSASPGEKVTMTCRASSSVSYLHWYQQKPGSSPKPWISATSNLASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQWSSNPLSFGGGTKLELK

Entity 8 Entity 8 polymer

Description description	5F5 heavy chain
Molecular weight formula_weight	13506.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

EIQLQQSGPELVKPGASVKVSCKASGYSFTDYNIYWVKQSHGKSLEWIGYVDPYNGNTNYNQKFKGKATLTVDKSSSTAFMHLNSLTSEVSTVYYCARGGGYYGGGYYGMDYWGQGTSVTVSS

Entity 9 Entity 9 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	7x3cB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	7x3cE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7x3cF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7x3cH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7x3cL01
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	3.03 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	81761

Cryo-EM structure of Coxsackievirus B1 muture virion in complex with nAbs 8A10 and 5F5 (CVB1-M:8A10:5F5)

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

Virion protein 1

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

Capsid protein 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

7x3c__assembly_1__model_1

7x3c__assembly_1__model_1 | I(q)

7x3c__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 (9)

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

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 non-polymer

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)