7x3c

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

Method: ELECTRON MICROSCOPY Dmax: 119.2 Å Quality: GOOD

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

Virion protein 1

OrganismNot specified

UniProt W8GTF7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 480 PDB declaration: 480-meric(480) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded 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 PLM PALMITIC ACID × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded 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 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
3 Protein heterocomplex Heteromer Protein × 40 PDB declaration: 40-meric(40) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded 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 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
4 Protein heterocomplex Heteromer Protein × 48 PDB declaration: 48-meric(48) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded 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 PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
5 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded 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 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

25 other PDB entries and 125 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 480 PDB declaration: 480-meric(480) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded 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 PLM PALMITIC ACID × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded 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 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
3 Protein heterocomplex Heteromer Protein × 40 PDB declaration: 40-meric(40) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded 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 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
4 Protein heterocomplex Heteromer Protein × 48 PDB declaration: 48-meric(48) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded 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 PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
5 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded 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 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

23 other PDB entries and 115 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 480 PDB declaration: 480-meric(480) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded 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 PLM PALMITIC ACID × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded 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 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
3 Protein heterocomplex Heteromer Protein × 40 PDB declaration: 40-meric(40) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded 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 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
4 Protein heterocomplex Heteromer Protein × 48 PDB declaration: 48-meric(48) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded 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 PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
5 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded 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 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

23 other PDB entries and 115 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 480 PDB declaration: 480-meric(480) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded 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 PLM PALMITIC ACID × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded 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 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
3 Protein heterocomplex Heteromer Protein × 40 PDB declaration: 40-meric(40) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded 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 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
4 Protein heterocomplex Heteromer Protein × 48 PDB declaration: 48-meric(48) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded 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 PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å
5 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded 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 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.03 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

14 other PDB entries and 70 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

SAXS profile for 7x3c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7x3c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7x3c
Deposition date deposition_date2022-02-28
Structure title titleCryo-EM structure of Coxsackievirus B1 muture virion in complex with nAbs 8A10 and 5F5 (CVB1-M:8A10:5F5)
Keywords keywordsCoxsackievirus B1, Neutralizing antibody, Cryo-EM, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.40
Radius of gyration Rg (electron density) rg_electron33.55
Forward intensity I(0) i0313422000.00
Molecular weight molecular_weight140630.0 kDa
Excluded volume excluded_volume175000 ų
Envelope volume envelope_volume227190 ų
Hydration-shell volume shell_volume54376 ų
Envelope diameter envelope_diameter130.8
Shell Rg shell_rg41.68
Envelope Rg envelope_rg33.97
Shape Rg shape_rg33.52
Total Rg total_rg34.25
Total atoms total_atoms9890
Residues n_residues1265
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax119.2
Rg (real space) rg_real34.27
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real3.1340e+08
I(0) uncertainty (real space) i0_real_error5.9700e+06
Rg (reciprocal space) rg_reciprocal34.35
I(0) (reciprocal space) i0_reciprocal313400000.0000
Solution quality estimate total_estimate0.8658
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.0
Skewness Skewness skewness0.226
Kurtosis Kurtosis kurtosis-0.316
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha71970000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id7x3cB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id7x3cE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7x3cF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7x3cH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7x3cL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)