7x3e

Cryo-EM structure of Coxsackievirus B1 pre-A-particle in complex with nAb 9A3 (CVB1-pre-A:9A3)

Method: ELECTRON MICROSCOPY Dmax: 102.5 Å Quality: EXCELLENT

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 × 360 PDB declaration: 360-meric(360) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded VP2 × 60 (A0A2S0RQC2) VP3 × 60 (L7UV52) Capsid protein VP4 × 60 (A0A2S1FMR1) 9A3 heavy chain × 60 9A3 light chain × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded VP2 × 1 (A0A2S0RQC2) VP3 × 1 (L7UV52) Capsid protein VP4 × 1 (A0A2S1FMR1) 9A3 heavy chain × 1 9A3 light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
3 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded VP2 × 5 (A0A2S0RQC2) VP3 × 5 (L7UV52) Capsid protein VP4 × 5 (A0A2S1FMR1) 9A3 heavy chain × 5 9A3 light chain × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
4 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded VP2 × 6 (A0A2S0RQC2) VP3 × 6 (L7UV52) Capsid protein VP4 × 6 (A0A2S1FMR1) 9A3 heavy chain × 6 9A3 light chain × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
5 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded VP2 × 1 (A0A2S0RQC2) VP3 × 1 (L7UV52) Capsid protein VP4 × 1 (A0A2S1FMR1) 9A3 heavy chain × 1 9A3 light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 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 1
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 × 360 PDB declaration: 360-meric(360) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded Virion protein 1 × 60 (W8GTF7) VP3 × 60 (L7UV52) Capsid protein VP4 × 60 (A0A2S1FMR1) 9A3 heavy chain × 60 9A3 light chain × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded Virion protein 1 × 1 (W8GTF7) VP3 × 1 (L7UV52) Capsid protein VP4 × 1 (A0A2S1FMR1) 9A3 heavy chain × 1 9A3 light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
3 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded Virion protein 1 × 5 (W8GTF7) VP3 × 5 (L7UV52) Capsid protein VP4 × 5 (A0A2S1FMR1) 9A3 heavy chain × 5 9A3 light chain × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
4 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded Virion protein 1 × 6 (W8GTF7) VP3 × 6 (L7UV52) Capsid protein VP4 × 6 (A0A2S1FMR1) 9A3 heavy chain × 6 9A3 light chain × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
5 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded Virion protein 1 × 1 (W8GTF7) VP3 × 1 (L7UV52) Capsid protein VP4 × 1 (A0A2S1FMR1) 9A3 heavy chain × 1 9A3 light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 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 2
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 × 360 PDB declaration: 360-meric(360) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded Virion protein 1 × 60 (W8GTF7) VP2 × 60 (A0A2S0RQC2) Capsid protein VP4 × 60 (A0A2S1FMR1) 9A3 heavy chain × 60 9A3 light chain × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded Virion protein 1 × 1 (W8GTF7) VP2 × 1 (A0A2S0RQC2) Capsid protein VP4 × 1 (A0A2S1FMR1) 9A3 heavy chain × 1 9A3 light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
3 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded Virion protein 1 × 5 (W8GTF7) VP2 × 5 (A0A2S0RQC2) Capsid protein VP4 × 5 (A0A2S1FMR1) 9A3 heavy chain × 5 9A3 light chain × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
4 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded Virion protein 1 × 6 (W8GTF7) VP2 × 6 (A0A2S0RQC2) Capsid protein VP4 × 6 (A0A2S1FMR1) 9A3 heavy chain × 6 9A3 light chain × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
5 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded Virion protein 1 × 1 (W8GTF7) VP2 × 1 (A0A2S0RQC2) Capsid protein VP4 × 1 (A0A2S1FMR1) 9A3 heavy chain × 1 9A3 light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 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 3
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 × 360 PDB declaration: 360-meric(360) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded Virion protein 1 × 60 (W8GTF7) VP2 × 60 (A0A2S0RQC2) VP3 × 60 (L7UV52) 9A3 heavy chain × 60 9A3 light chain × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded Virion protein 1 × 1 (W8GTF7) VP2 × 1 (A0A2S0RQC2) VP3 × 1 (L7UV52) 9A3 heavy chain × 1 9A3 light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
3 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded Virion protein 1 × 5 (W8GTF7) VP2 × 5 (A0A2S0RQC2) VP3 × 5 (L7UV52) 9A3 heavy chain × 5 9A3 light chain × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
4 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded Virion protein 1 × 6 (W8GTF7) VP2 × 6 (A0A2S0RQC2) VP3 × 6 (L7UV52) 9A3 heavy chain × 6 9A3 light chain × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 Å
5 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 1–69 Not recorded Virion protein 1 × 1 (W8GTF7) VP2 × 1 (A0A2S0RQC2) VP3 × 1 (L7UV52) 9A3 heavy chain × 1 9A3 light chain × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.44 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 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.

SAXS scattering curve SAXS Profile

SAXS profile for 7x3e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7x3e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7x3e
Deposition date deposition_date2022-02-28
Structure title titleCryo-EM structure of Coxsackievirus B1 pre-A-particle in complex with nAb 9A3 (CVB1-pre-A:9A3)
Keywords keywordsCoxsackievirus B1, Neutralizing antiboy, Cryo-EM, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier33.05
Radius of gyration Rg (electron density) rg_electron32.11
Forward intensity I(0) i0213107000.00
Molecular weight molecular_weight115200.0 kDa
Excluded volume excluded_volume143360 ų
Envelope volume envelope_volume188970 ų
Hydration-shell volume shell_volume47776 ų
Envelope diameter envelope_diameter108.9
Shell Rg shell_rg40.04
Envelope Rg envelope_rg32.63
Shape Rg shape_rg32.09
Total Rg total_rg32.81
Total atoms total_atoms8101
Residues n_residues1041
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 dmax102.5
Rg (real space) rg_real32.89
Rg uncertainty (real space) rg_real_error0.60
I(0) (real space) i0_real2.1310e+08
I(0) uncertainty (real space) i0_real_error3.1590e+06
Rg (reciprocal space) rg_reciprocal32.96
I(0) (reciprocal space) i0_reciprocal213100000.0000
Solution quality estimate total_estimate0.9041
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.6
Skewness Skewness skewness0.194
Kurtosis Kurtosis kurtosis-0.509
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38330000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.912

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id7x3eB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id7x3eH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7x3eL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)