7x4k

Cryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (classified from CVB1 mature virion in complex with 8A10 and 9A3)

Method: ELECTRON MICROSCOPY Dmax: 106.3 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 × 300 PDB declaration: 300-meric(300) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded 9A3 heavy chain × 60 9A3 light chain × 60 Genome polyprotein × 60 (A0A7T7KAA0) VP3 × 60 (L7UV52) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded 9A3 heavy chain × 1 9A3 light chain × 1 Genome polyprotein × 1 (A0A7T7KAA0) VP3 × 1 (L7UV52) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded 9A3 heavy chain × 5 9A3 light chain × 5 Genome polyprotein × 5 (A0A7T7KAA0) VP3 × 5 (L7UV52) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded 9A3 heavy chain × 6 9A3 light chain × 6 Genome polyprotein × 6 (A0A7T7KAA0) VP3 × 6 (L7UV52) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–278 Not recorded 9A3 heavy chain × 1 9A3 light chain × 1 Genome polyprotein × 1 (A0A7T7KAA0) VP3 × 1 (L7UV52) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 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

Genome polyprotein

OrganismNot specified

UniProt A0A7T7KAA0

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 × 300 PDB declaration: 300-meric(300) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded 9A3 heavy chain × 60 9A3 light chain × 60 Virion protein 1 × 60 (W8GTF7) VP3 × 60 (L7UV52) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded 9A3 heavy chain × 1 9A3 light chain × 1 Virion protein 1 × 1 (W8GTF7) VP3 × 1 (L7UV52) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded 9A3 heavy chain × 5 9A3 light chain × 5 Virion protein 1 × 5 (W8GTF7) VP3 × 5 (L7UV52) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded 9A3 heavy chain × 6 9A3 light chain × 6 Virion protein 1 × 6 (W8GTF7) VP3 × 6 (L7UV52) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 70–332 Not recorded 9A3 heavy chain × 1 9A3 light chain × 1 Virion protein 1 × 1 (W8GTF7) VP3 × 1 (L7UV52) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 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.

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A7T7KAA0_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 × 300 PDB declaration: 300-meric(300) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded 9A3 heavy chain × 60 9A3 light chain × 60 Virion protein 1 × 60 (W8GTF7) Genome polyprotein × 60 (A0A7T7KAA0) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded 9A3 heavy chain × 1 9A3 light chain × 1 Virion protein 1 × 1 (W8GTF7) Genome polyprotein × 1 (A0A7T7KAA0) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded 9A3 heavy chain × 5 9A3 light chain × 5 Virion protein 1 × 5 (W8GTF7) Genome polyprotein × 5 (A0A7T7KAA0) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded 9A3 heavy chain × 6 9A3 light chain × 6 Virion protein 1 × 6 (W8GTF7) Genome polyprotein × 6 (A0A7T7KAA0) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 333–570 Not recorded 9A3 heavy chain × 1 9A3 light chain × 1 Virion protein 1 × 1 (W8GTF7) Genome polyprotein × 1 (A0A7T7KAA0) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 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

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 7x4k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7x4k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7x4k
Deposition date deposition_date2022-03-02
Structure title titleCryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (classified from CVB1 mature virion in complex with 8A10 and 9A3)
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_guinier32.63
Radius of gyration Rg (electron density) rg_electron31.83
Forward intensity I(0) i0155433000.00
Molecular weight molecular_weight98929.0 kDa
Excluded volume excluded_volume123550 ų
Envelope volume envelope_volume163750 ų
Hydration-shell volume shell_volume42741 ų
Envelope diameter envelope_diameter113.5
Shell Rg shell_rg38.76
Envelope Rg envelope_rg32.33
Shape Rg shape_rg31.80
Total Rg total_rg32.51
Total atoms total_atoms6957
Residues n_residues896
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 dmax106.3
Rg (real space) rg_real32.55
Rg uncertainty (real space) rg_real_error0.83
I(0) (real space) i0_real1.5540e+08
I(0) uncertainty (real space) i0_real_error2.3580e+06
Rg (reciprocal space) rg_reciprocal32.59
I(0) (reciprocal space) i0_reciprocal155400000.0000
Solution quality estimate total_estimate0.9000
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.1
Skewness Skewness skewness0.254
Kurtosis Kurtosis kurtosis-0.471
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha32140000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.969

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)