1jew

CRYO-EM STRUCTURE OF COXSACKIEVIRUS B3(M STRAIN) WITH ITS CELLULAR RECEPTOR, COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR (CAR).

Method: ELECTRON MICROSCOPY Dmax: 94.0 Å Quality: EXCELLENT

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

COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR

Homo sapiens

UniProt P78310

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 21–140 Fragment:Residues 21-140 COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1 × 60 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP2 × 60 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP3 × 60 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP4 × 60 (Q66282) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR 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;298 K;WARNING: THIS IS AN CRYO-ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE PDB FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION, temperature 298K Resolution 22.00 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 21–140 Fragment:Residues 21-140 COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1 × 1 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP2 × 1 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP3 × 1 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP4 × 1 (Q66282) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR 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;298 K;WARNING: THIS IS AN CRYO-ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE PDB FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION, temperature 298K Resolution 22.00 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain R; UniProt 21–140 Fragment:Residues 21-140 COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1 × 5 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP2 × 5 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP3 × 5 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP4 × 5 (Q66282) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR 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;298 K;WARNING: THIS IS AN CRYO-ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE PDB FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION, temperature 298K Resolution 22.00 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain R; UniProt 21–140 Fragment:Residues 21-140 COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1 × 6 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP2 × 6 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP3 × 6 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP4 × 6 (Q66282) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR 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;298 K;WARNING: THIS IS AN CRYO-ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE PDB FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION, temperature 298K Resolution 22.00 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 21–140 Fragment:Residues 21-140 COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1 × 1 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP2 × 1 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP3 × 1 (Q66282) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP4 × 1 (Q66282) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR 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;298 K;WARNING: THIS IS AN CRYO-ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE PDB FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION, temperature 298K 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.

20 other PDB entries and 63 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CXAR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 1–120; UniProt 21–140

COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1

Coxsackievirus B3 (strain Woodruff)

UniProt Q66282

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 571–851 Chain 2; UniProt 70–332 Chain 3; UniProt 333–570 Chain 4; UniProt 2–69 Fragment:Residues 571-851 Fragment:Residues 70-332 Fragment:Residues 333-570 Fragment:Residues 2-69 COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR × 60 (P78310) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR 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;298 K;WARNING: THIS IS AN CRYO-ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE PDB FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION, temperature 298K Resolution 22.00 Å
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain 1; UniProt 571–851 Chain 2; UniProt 70–332 Chain 3; UniProt 333–570 Chain 4; UniProt 2–69 Fragment:Residues 571-851 Fragment:Residues 70-332 Fragment:Residues 333-570 Fragment:Residues 2-69 COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR × 1 (P78310) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR 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;298 K;WARNING: THIS IS AN CRYO-ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE PDB FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION, temperature 298K Resolution 22.00 Å
3 Protein heterocomplex Heteromer Protein × 25 PDB declaration: 25-meric(25) Consistent with protein copy count Chain 1; UniProt 571–851 Chain 2; UniProt 70–332 Chain 3; UniProt 333–570 Chain 4; UniProt 2–69 Fragment:Residues 571-851 Fragment:Residues 70-332 Fragment:Residues 333-570 Fragment:Residues 2-69 COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR × 5 (P78310) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR 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;298 K;WARNING: THIS IS AN CRYO-ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE PDB FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION, temperature 298K Resolution 22.00 Å
4 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain 1; UniProt 571–851 Chain 2; UniProt 70–332 Chain 3; UniProt 333–570 Chain 4; UniProt 2–69 Fragment:Residues 571-851 Fragment:Residues 70-332 Fragment:Residues 333-570 Fragment:Residues 2-69 COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR × 6 (P78310) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR 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;298 K;WARNING: THIS IS AN CRYO-ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE PDB FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION, temperature 298K Resolution 22.00 Å
5 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain 1; UniProt 571–851 Chain 2; UniProt 70–332 Chain 3; UniProt 333–570 Chain 4; UniProt 2–69 Fragment:Residues 571-851 Fragment:Residues 70-332 Fragment:Residues 333-570 Fragment:Residues 2-69 COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR × 1 (P78310) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR 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;298 K;WARNING: THIS IS AN CRYO-ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE PDB FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION, temperature 298K 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.

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

View Construct and Data Evidence
UniProt name POLG_CXB3W
Isoform
PDB entities 2, 3, 4, 5
Chains and sequence ranges Author chain 1; PDBConstruct 1–281; UniProt 571–851 Author chain 2; PDBConstruct 1–263; UniProt 70–332 Author chain 3; PDBConstruct 1–238; UniProt 333–570 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 1jew

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1jew
Deposition date deposition_date2001-06-19
Structure title titleCRYO-EM STRUCTURE OF COXSACKIEVIRUS B3(M STRAIN) WITH ITS CELLULAR RECEPTOR, COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR (CAR).
Keywords keywordsCOXSACKIEVIRUS B3, CVB3, CAR, CRYO-EM STRUCTURE, 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_guinier30.31
Radius of gyration Rg (electron density) rg_electron29.56
Forward intensity I(0) i0168341000.00
Molecular weight molecular_weight104010.0 kDa
Excluded volume excluded_volume126510 ų
Envelope volume envelope_volume104990 ų
Hydration-shell volume shell_volume31706 ų
Envelope diameter envelope_diameter101.4
Shell Rg shell_rg34.39
Envelope Rg envelope_rg28.44
Shape Rg shape_rg29.76
Total Rg total_rg29.88
Total atoms total_atoms
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 dmax94.0
Rg (real space) rg_real30.23
Rg uncertainty (real space) rg_real_error0.48
I(0) (real space) i0_real1.6830e+08
I(0) uncertainty (real space) i0_real_error2.4310e+06
Rg (reciprocal space) rg_reciprocal30.27
I(0) (reciprocal space) i0_reciprocal168300000.0000
Solution quality estimate total_estimate0.9064
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.1
Skewness Skewness skewness0.274
Kurtosis Kurtosis kurtosis-0.403
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25500000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.954

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_idd1jew1_
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_idd1jew2_
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_idd1jew3_
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_idd1jew4_
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_idd1jewr_
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 (4)

9. Files and Curves (10)