1dgi

Cryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155

Method: ELECTRON MICROSCOPY Dmax: 129.2 Å Quality: REASONABLE

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 28–329 Fragment:THREE EXTRACELLULAR DOMAINS OF CD155 VP1 × 60 (P03300) VP2 × 60 (P03300) VP3 × 60 (P03300) VP4 × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions:ELECTRON MICROSCOPY RECONSTRUCTION;pH 7.5;WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION Resolution 22.00 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 28–329 Fragment:THREE EXTRACELLULAR DOMAINS OF CD155 VP1 × 1 (P03300) VP2 × 1 (P03300) VP3 × 1 (P03300) VP4 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions:ELECTRON MICROSCOPY RECONSTRUCTION;pH 7.5;WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION Resolution 22.00 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain R; UniProt 28–329 Fragment:THREE EXTRACELLULAR DOMAINS OF CD155 VP1 × 5 (P03300) VP2 × 5 (P03300) VP3 × 5 (P03300) VP4 × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions:ELECTRON MICROSCOPY RECONSTRUCTION;pH 7.5;WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION Resolution 22.00 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain R; UniProt 28–329 Fragment:THREE EXTRACELLULAR DOMAINS OF CD155 VP1 × 6 (P03300) VP2 × 6 (P03300) VP3 × 6 (P03300) VP4 × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions:ELECTRON MICROSCOPY RECONSTRUCTION;pH 7.5;WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION Resolution 22.00 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 28–329 Fragment:THREE EXTRACELLULAR DOMAINS OF CD155 VP1 × 1 (P03300) VP2 × 1 (P03300) VP3 × 1 (P03300) VP4 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions:ELECTRON MICROSCOPY RECONSTRUCTION;pH 7.5;WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION Resolution 22.00 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 1–302; UniProt 28–329

VP1

Human poliovirus 1

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 598–880 Chain 2; UniProt 73–340 Chain 3; UniProt 341–575 Not recorded POLIOVIRUS RECEPTOR × 60 (P15151) VP4 × 60 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions:ELECTRON MICROSCOPY RECONSTRUCTION;pH 7.5;WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION Resolution 22.00 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain 1; UniProt 598–880 Chain 2; UniProt 73–340 Chain 3; UniProt 341–575 Not recorded POLIOVIRUS RECEPTOR × 1 (P15151) VP4 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions:ELECTRON MICROSCOPY RECONSTRUCTION;pH 7.5;WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION Resolution 22.00 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain 1; UniProt 598–880 Chain 2; UniProt 73–340 Chain 3; UniProt 341–575 Not recorded POLIOVIRUS RECEPTOR × 5 (P15151) VP4 × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions:ELECTRON MICROSCOPY RECONSTRUCTION;pH 7.5;WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION Resolution 22.00 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain 1; UniProt 598–880 Chain 2; UniProt 73–340 Chain 3; UniProt 341–575 Not recorded POLIOVIRUS RECEPTOR × 6 (P15151) VP4 × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions:ELECTRON MICROSCOPY RECONSTRUCTION;pH 7.5;WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION Resolution 22.00 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain 1; UniProt 598–880 Chain 2; UniProt 73–340 Chain 3; UniProt 341–575 Not recorded POLIOVIRUS RECEPTOR × 1 (P15151) VP4 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions:ELECTRON MICROSCOPY RECONSTRUCTION;pH 7.5;WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION Resolution 22.00 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 POLH_POL1M
Isoform
PDB entities 2, 3, 4
Chains and sequence ranges Author chain 1; PDBConstruct 1–5; UniProt 598–880 Author chain 2; PDBConstruct 1–268; UniProt 73–340 Author chain 3; PDBConstruct 1–235; UniProt 341–575

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 1dgi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dgi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dgi
Deposition date deposition_date1999-11-24
Structure title titleCryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155
Keywords keywordsCD155, PVR, HUMAN POLIOVIRUS, POLIOVIRUS-RECEPTOR COMPLEX, Icosahedral virus, Virus-Receptor COMPLEX; Virus/Receptor
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier44.84
Radius of gyration Rg (electron density) rg_electron46.64
Forward intensity I(0) i0243470000.00
Molecular weight molecular_weight127260.0 kDa
Excluded volume excluded_volume155120 ų
Envelope volume envelope_volume156440 ų
Hydration-shell volume shell_volume34516 ų
Envelope diameter envelope_diameter178.2
Shell Rg shell_rg39.57
Envelope Rg envelope_rg49.43
Shape Rg shape_rg46.93
Total Rg total_rg46.34
Total atoms total_atoms1
Residues n_residues
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 dmax129.2
Rg (real space) rg_real40.57
Rg uncertainty (real space) rg_real_error0.68
I(0) (real space) i0_real2.3260e+08
I(0) uncertainty (real space) i0_real_error4.2810e+06
Rg (reciprocal space) rg_reciprocal44.85
I(0) (reciprocal space) i0_reciprocal243000000.0000
Solution quality estimate total_estimate0.6352
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary36.9
Skewness Skewness skewness0.760
Kurtosis Kurtosis kurtosis0.042
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0828
Highest regularization parameter α highest_alpha17630000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.651; Stabil: 0.929; Sysdev: 0.000; Positv: 1.000; Valcen: 0.845; Smooth: 0.706

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd1dgi1_
Class classi — Low resolution protein structures
Fold Fold foldi.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
Family Family familyi.6.1.1 — Viruses and virus-receptor complexes
Domain ID domain_idd1dgi2_
Class classi — Low resolution protein structures
Fold Fold foldi.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
Family Family familyi.6.1.1 — Viruses and virus-receptor complexes
Domain ID domain_idd1dgi3_
Class classi — Low resolution protein structures
Fold Fold foldi.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
Family Family familyi.6.1.1 — Viruses and virus-receptor complexes
Domain ID domain_idd1dgi4_
Class classi — Low resolution protein structures
Fold Fold foldi.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
Family Family familyi.6.1.1 — Viruses and virus-receptor complexes
Domain ID domain_idd1dgir_
Class classi — Low resolution protein structures
Fold Fold foldi.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
Family Family familyi.6.1.1 — Viruses and virus-receptor complexes

8. Citations (3)

9. Files and Curves (10)