3epc

CryoEM structure of poliovirus receptor bound to poliovirus type 1

Method: ELECTRON MICROSCOPY Dmax: 142.2 Å Quality: GOOD

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

Poliovirus receptor

Homo sapiens

UniProt P15151

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 R; UniProt 30–242 Fragment:Poliovirus receptor CD155 D1D2 Mutation:N105D, N120S, N188Q, N218Q, N237S Protein VP1 × 60 (P03300) Protein VP2 × 60 (P03300) Protein VP4 × 60 (P03300) Protein VP3 × 60 (P03300) SPH SPHINGOSINE × 60 MYR MYRISTIC ACID × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.00 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 30–242 Fragment:Poliovirus receptor CD155 D1D2 Mutation:N105D, N120S, N188Q, N218Q, N237S Protein VP1 × 1 (P03300) Protein VP2 × 1 (P03300) Protein VP4 × 1 (P03300) Protein VP3 × 1 (P03300) SPH SPHINGOSINE × 1 MYR MYRISTIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.00 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain R; UniProt 30–242 Fragment:Poliovirus receptor CD155 D1D2 Mutation:N105D, N120S, N188Q, N218Q, N237S Protein VP1 × 5 (P03300) Protein VP2 × 5 (P03300) Protein VP4 × 5 (P03300) Protein VP3 × 5 (P03300) SPH SPHINGOSINE × 5 MYR MYRISTIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.00 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain R; UniProt 30–242 Fragment:Poliovirus receptor CD155 D1D2 Mutation:N105D, N120S, N188Q, N218Q, N237S Protein VP1 × 6 (P03300) Protein VP2 × 6 (P03300) Protein VP4 × 6 (P03300) Protein VP3 × 6 (P03300) SPH SPHINGOSINE × 6 MYR MYRISTIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.00 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 30–242 Fragment:Poliovirus receptor CD155 D1D2 Mutation:N105D, N120S, N188Q, N218Q, N237S Protein VP1 × 1 (P03300) Protein VP2 × 1 (P03300) Protein VP4 × 1 (P03300) Protein VP3 × 1 (P03300) SPH SPHINGOSINE × 1 MYR MYRISTIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.00 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.

12 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PVR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 1–213; UniProt 30–242

Protein VP1

Human poliovirus 1 Mahoney

UniProt P03300

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 1; UniProt 599–881 Chain 2; UniProt 74–341 Chain 3; UniProt 342–576 Chain 4; UniProt 2–69 Not recorded Poliovirus receptor × 60 (P15151) SPH SPHINGOSINE × 60 MYR MYRISTIC ACID × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.00 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain 1; UniProt 599–881 Chain 2; UniProt 74–341 Chain 3; UniProt 342–576 Chain 4; UniProt 2–69 Not recorded Poliovirus receptor × 1 (P15151) SPH SPHINGOSINE × 1 MYR MYRISTIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.00 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain 1; UniProt 599–881 Chain 2; UniProt 74–341 Chain 3; UniProt 342–576 Chain 4; UniProt 2–69 Not recorded Poliovirus receptor × 5 (P15151) SPH SPHINGOSINE × 5 MYR MYRISTIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.00 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain 1; UniProt 599–881 Chain 2; UniProt 74–341 Chain 3; UniProt 342–576 Chain 4; UniProt 2–69 Not recorded Poliovirus receptor × 6 (P15151) SPH SPHINGOSINE × 6 MYR MYRISTIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.00 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain 1; UniProt 599–881 Chain 2; UniProt 74–341 Chain 3; UniProt 342–576 Chain 4; UniProt 2–69 Not recorded Poliovirus receptor × 1 (P15151) SPH SPHINGOSINE × 1 MYR MYRISTIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions:Cryogen ETHANE Resolution 8.00 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.

80 other PDB entries and 246 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_POL1M
Isoform
PDB entities 2, 3, 4, 5
Chains and sequence ranges Author chain 1; PDBConstruct 1–283; UniProt 599–881 Author chain 2; PDBConstruct 1–268; UniProt 74–341 Author chain 4; PDBConstruct 1–68; UniProt 2–69 Author chain 3; PDBConstruct 1–235; UniProt 342–576

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 3epc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3epc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3epc
Deposition date deposition_date2008-09-29
Structure title titleCryoEM structure of poliovirus receptor bound to poliovirus type 1
Keywords keywords;CD155 structure Immunoglobulin Superfamily, poliovirus capsid jelly role, Cell adhesion, Cell membrane, Glycoprotein, Host-virus interaction, Immunoglobulin domain, Membrane, Receptor, Secreted, Transmembrane, VIRAL PROTEIN, VIRUS ;; VIRUS
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier36.32
Radius of gyration Rg (electron density) rg_electron36.27
Forward intensity I(0) i0214140000.00
Molecular weight molecular_weight117830.0 kDa
Excluded volume excluded_volume147470 ų
Envelope volume envelope_volume202790 ų
Hydration-shell volume shell_volume48374 ų
Envelope diameter envelope_diameter149.7
Shell Rg shell_rg40.44
Envelope Rg envelope_rg37.62
Shape Rg shape_rg36.23
Total Rg total_rg36.70
Total atoms total_atoms8292
Residues n_residues1061
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 dmax142.2
Rg (real space) rg_real36.58
Rg uncertainty (real space) rg_real_error1.38
I(0) (real space) i0_real2.1410e+08
I(0) uncertainty (real space) i0_real_error3.7160e+06
Rg (reciprocal space) rg_reciprocal36.42
I(0) (reciprocal space) i0_reciprocal214100000.0000
Solution quality estimate total_estimate0.7908
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.8
Skewness Skewness skewness0.641
Kurtosis Kurtosis kurtosis0.412
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha32550000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.514; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.755; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)