8e8r

9H2 Fab-Sabin poliovirus 3 complex

Method: ELECTRON MICROSCOPY Dmax: 102.3 Å Quality: REASONABLE

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

Capsid protein VP1

OrganismNot specified

UniProt B2X7G7

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 1; UniProt 22–300 Not recorded Capsid protein VP2 × 60 (P03302) Capsid protein VP3 × 60 (A0A2H4WRH7) Capsid protein VP4 × 60 (A0A2H4Z5W5) 9H2 Fab heavy chain × 60 9H2 Fab light chain × 60 PLM PALMITIC ACID × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain 1; UniProt 22–300 Not recorded Capsid protein VP2 × 1 (P03302) Capsid protein VP3 × 1 (A0A2H4WRH7) Capsid protein VP4 × 1 (A0A2H4Z5W5) 9H2 Fab heavy chain × 1 9H2 Fab light chain × 1 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
3 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain 1; UniProt 22–300 Not recorded Capsid protein VP2 × 5 (P03302) Capsid protein VP3 × 5 (A0A2H4WRH7) Capsid protein VP4 × 5 (A0A2H4Z5W5) 9H2 Fab heavy chain × 5 9H2 Fab light chain × 5 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
4 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain 1; UniProt 22–300 Not recorded Capsid protein VP2 × 6 (P03302) Capsid protein VP3 × 6 (A0A2H4WRH7) Capsid protein VP4 × 6 (A0A2H4Z5W5) 9H2 Fab heavy chain × 6 9H2 Fab light chain × 6 PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
5 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain 1; UniProt 22–300 Not recorded Capsid protein VP2 × 1 (P03302) Capsid protein VP3 × 1 (A0A2H4WRH7) Capsid protein VP4 × 1 (A0A2H4Z5W5) 9H2 Fab heavy chain × 1 9H2 Fab light chain × 1 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name B2X7G7_9ENTO
Isoform
PDB entities 1
Chains and sequence ranges Author chain 1; PDBConstruct 1–279; UniProt 22–300

Capsid protein VP2

OrganismNot specified

UniProt P03302

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 2; UniProt 78–340 Not recorded Capsid protein VP1 × 60 (B2X7G7) Capsid protein VP3 × 60 (A0A2H4WRH7) Capsid protein VP4 × 60 (A0A2H4Z5W5) 9H2 Fab heavy chain × 60 9H2 Fab light chain × 60 PLM PALMITIC ACID × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain 2; UniProt 78–340 Not recorded Capsid protein VP1 × 1 (B2X7G7) Capsid protein VP3 × 1 (A0A2H4WRH7) Capsid protein VP4 × 1 (A0A2H4Z5W5) 9H2 Fab heavy chain × 1 9H2 Fab light chain × 1 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
3 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain 2; UniProt 78–340 Not recorded Capsid protein VP1 × 5 (B2X7G7) Capsid protein VP3 × 5 (A0A2H4WRH7) Capsid protein VP4 × 5 (A0A2H4Z5W5) 9H2 Fab heavy chain × 5 9H2 Fab light chain × 5 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
4 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain 2; UniProt 78–340 Not recorded Capsid protein VP1 × 6 (B2X7G7) Capsid protein VP3 × 6 (A0A2H4WRH7) Capsid protein VP4 × 6 (A0A2H4Z5W5) 9H2 Fab heavy chain × 6 9H2 Fab light chain × 6 PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
5 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain 2; UniProt 78–340 Not recorded Capsid protein VP1 × 1 (B2X7G7) Capsid protein VP3 × 1 (A0A2H4WRH7) Capsid protein VP4 × 1 (A0A2H4Z5W5) 9H2 Fab heavy chain × 1 9H2 Fab light chain × 1 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 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.

11 other PDB entries and 57 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_POL3L
Isoform
PDB entities 2
Chains and sequence ranges Author chain 2; PDBConstruct 1–263; UniProt 78–340

Capsid protein VP3

OrganismNot specified

UniProt A0A2H4WRH7

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 3; UniProt 341–575 Not recorded Capsid protein VP1 × 60 (B2X7G7) Capsid protein VP2 × 60 (P03302) Capsid protein VP4 × 60 (A0A2H4Z5W5) 9H2 Fab heavy chain × 60 9H2 Fab light chain × 60 PLM PALMITIC ACID × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain 3; UniProt 341–575 Not recorded Capsid protein VP1 × 1 (B2X7G7) Capsid protein VP2 × 1 (P03302) Capsid protein VP4 × 1 (A0A2H4Z5W5) 9H2 Fab heavy chain × 1 9H2 Fab light chain × 1 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
3 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain 3; UniProt 341–575 Not recorded Capsid protein VP1 × 5 (B2X7G7) Capsid protein VP2 × 5 (P03302) Capsid protein VP4 × 5 (A0A2H4Z5W5) 9H2 Fab heavy chain × 5 9H2 Fab light chain × 5 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
4 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain 3; UniProt 341–575 Not recorded Capsid protein VP1 × 6 (B2X7G7) Capsid protein VP2 × 6 (P03302) Capsid protein VP4 × 6 (A0A2H4Z5W5) 9H2 Fab heavy chain × 6 9H2 Fab light chain × 6 PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
5 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain 3; UniProt 341–575 Not recorded Capsid protein VP1 × 1 (B2X7G7) Capsid protein VP2 × 1 (P03302) Capsid protein VP4 × 1 (A0A2H4Z5W5) 9H2 Fab heavy chain × 1 9H2 Fab light chain × 1 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 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.

1 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A2H4WRH7_9ENTO
Isoform
PDB entities 3
Chains and sequence ranges Author chain 3; PDBConstruct 1–235; UniProt 341–575

Capsid protein VP4

OrganismNot specified

UniProt A0A2H4Z5W5

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 4; UniProt 2–69 Not recorded Capsid protein VP1 × 60 (B2X7G7) Capsid protein VP2 × 60 (P03302) Capsid protein VP3 × 60 (A0A2H4WRH7) 9H2 Fab heavy chain × 60 9H2 Fab light chain × 60 PLM PALMITIC ACID × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain 4; UniProt 2–69 Not recorded Capsid protein VP1 × 1 (B2X7G7) Capsid protein VP2 × 1 (P03302) Capsid protein VP3 × 1 (A0A2H4WRH7) 9H2 Fab heavy chain × 1 9H2 Fab light chain × 1 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
3 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain 4; UniProt 2–69 Not recorded Capsid protein VP1 × 5 (B2X7G7) Capsid protein VP2 × 5 (P03302) Capsid protein VP3 × 5 (A0A2H4WRH7) 9H2 Fab heavy chain × 5 9H2 Fab light chain × 5 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
4 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain 4; UniProt 2–69 Not recorded Capsid protein VP1 × 6 (B2X7G7) Capsid protein VP2 × 6 (P03302) Capsid protein VP3 × 6 (A0A2H4WRH7) 9H2 Fab heavy chain × 6 9H2 Fab light chain × 6 PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 Å
5 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain 4; UniProt 2–69 Not recorded Capsid protein VP1 × 1 (B2X7G7) Capsid protein VP2 × 1 (P03302) Capsid protein VP3 × 1 (A0A2H4WRH7) 9H2 Fab heavy chain × 1 9H2 Fab light chain × 1 PLM PALMITIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.66 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.

1 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A2H4Z5W5_9ENTO
Isoform
PDB entities 4
Chains and sequence ranges Author chain 4; 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.

SAXS scattering curve SAXS Profile

SAXS profile for 8e8r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8e8r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8e8r
Deposition date deposition_date2022-08-25
Structure title title9H2 Fab-Sabin poliovirus 3 complex
Keywords keywordsComplex, Fab, poliovirus, neutralizing, VIRUS-IMMUNE SYSTEM complex; VIRUS/IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier32.75
Radius of gyration Rg (electron density) rg_electron31.87
Forward intensity I(0) i0219299000.00
Molecular weight molecular_weight118470.0 kDa
Excluded volume excluded_volume148020 ų
Envelope volume envelope_volume186400 ų
Hydration-shell volume shell_volume47258 ų
Envelope diameter envelope_diameter109.3
Shell Rg shell_rg39.97
Envelope Rg envelope_rg32.29
Shape Rg shape_rg31.84
Total Rg total_rg32.60
Total atoms total_atoms8343
Residues n_residues1068
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 dmax102.3
Rg (real space) rg_real32.63
Rg uncertainty (real space) rg_real_error0.63
I(0) (real space) i0_real2.1930e+08
I(0) uncertainty (real space) i0_real_error3.5730e+06
Rg (reciprocal space) rg_reciprocal32.68
I(0) (reciprocal space) i0_reciprocal219300000.0000
Solution quality estimate total_estimate0.6828
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.4
Skewness Skewness skewness0.232
Kurtosis Kurtosis kurtosis-0.504
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha45230000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 0.049; Positv: 1.000; Valcen: 0.999; Smooth: 0.903

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id8e8r101
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id8e8r201
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id8e8rH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8e8rL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)