3j8f

Cryo-EM reconstruction of poliovirus-receptor complex

Method: ELECTRON MICROSCOPY Dmax: 156.0 Å Quality: REASONABLE

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

Capsid protein VP1

OrganismNot specified

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 Other combination Heteromer Protein × 300 其他Polymer 360 PDB declaration: 300-meric(300) Consistent with protein copy count Chain 1; UniProt 580–881 Chain 2; UniProt 70–341 Chain 3; UniProt 342–579 Chain 4; UniProt 2–69 Fragment:UNP residues 580-881 Fragment:UNP residues 70-341 Fragment:UNP residues 342-579 Fragment:UNP residues 2-69 Non-standard monomer:Yes (specific site not provided by mmCIF) Poliovirus receptor × 60 (P15151) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 60 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 60 ELECTRON MICROSCOPY cryo-EM buffer:PBS;pH 7;PBS cryo-EM vitrification conditions:Sample mixed and frozen within 2 minutes.;120 K;Cryogen ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. Resolution 3.70 Å
2 Other combination Heteromer Protein × 5 其他Polymer 6 PDB declaration: pentameric(5) Consistent with protein copy count Chain 1; UniProt 580–881 Chain 2; UniProt 70–341 Chain 3; UniProt 342–579 Chain 4; UniProt 2–69 Fragment:UNP residues 580-881 Fragment:UNP residues 70-341 Fragment:UNP residues 342-579 Fragment:UNP residues 2-69 Non-standard monomer:Yes (specific site not provided by mmCIF) Poliovirus receptor × 1 (P15151) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:PBS;pH 7;PBS cryo-EM vitrification conditions:Sample mixed and frozen within 2 minutes.;120 K;Cryogen ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. Resolution 3.70 Å
3 Other combination Heteromer Protein × 25 其他Polymer 30 PDB declaration: 25-meric(25) Consistent with protein copy count Chain 1; UniProt 580–881 Chain 2; UniProt 70–341 Chain 3; UniProt 342–579 Chain 4; UniProt 2–69 Fragment:UNP residues 580-881 Fragment:UNP residues 70-341 Fragment:UNP residues 342-579 Fragment:UNP residues 2-69 Non-standard monomer:Yes (specific site not provided by mmCIF) Poliovirus receptor × 5 (P15151) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 5 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY cryo-EM buffer:PBS;pH 7;PBS cryo-EM vitrification conditions:Sample mixed and frozen within 2 minutes.;120 K;Cryogen ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. Resolution 3.70 Å
4 Other combination Heteromer Protein × 30 其他Polymer 36 PDB declaration: 30-meric(30) Consistent with protein copy count Chain 1; UniProt 580–881 Chain 2; UniProt 70–341 Chain 3; UniProt 342–579 Chain 4; UniProt 2–69 Fragment:UNP residues 580-881 Fragment:UNP residues 70-341 Fragment:UNP residues 342-579 Fragment:UNP residues 2-69 Non-standard monomer:Yes (specific site not provided by mmCIF) Poliovirus receptor × 6 (P15151) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 6 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer:PBS;pH 7;PBS cryo-EM vitrification conditions:Sample mixed and frozen within 2 minutes.;120 K;Cryogen ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. Resolution 3.70 Å
5 Other combination Heteromer Protein × 5 其他Polymer 6 PDB declaration: pentameric(5) Consistent with protein copy count Chain 1; UniProt 580–881 Chain 2; UniProt 70–341 Chain 3; UniProt 342–579 Chain 4; UniProt 2–69 Fragment:UNP residues 580-881 Fragment:UNP residues 70-341 Fragment:UNP residues 342-579 Fragment:UNP residues 2-69 Non-standard monomer:Yes (specific site not provided by mmCIF) Poliovirus receptor × 1 (P15151) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:PBS;pH 7;PBS cryo-EM vitrification conditions:Sample mixed and frozen within 2 minutes.;120 K;Cryogen ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. Resolution 3.70 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 1, 2, 3, 4
Chains and sequence ranges Author chain 1; PDBConstruct 1–302; UniProt 580–881 Author chain 2; PDBConstruct 1–272; UniProt 70–341 Author chain 3; PDBConstruct 1–238; UniProt 342–579 Author chain 4; PDBConstruct 2–69; UniProt 2–69

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 Other combination Heteromer Protein × 300 其他Polymer 360 PDB declaration: 300-meric(300) Consistent with protein copy count Chain 7; UniProt 1–417 Not recorded Capsid protein VP1 × 60 (P03300) Capsid protein VP2 × 60 (P03300) Capsid protein VP3 × 60 (P03300) Capsid protein VP4 × 60 (P03300) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 60 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 60 ELECTRON MICROSCOPY cryo-EM buffer:PBS;pH 7;PBS cryo-EM vitrification conditions:Sample mixed and frozen within 2 minutes.;120 K;Cryogen ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. Resolution 3.70 Å
2 Other combination Heteromer Protein × 5 其他Polymer 6 PDB declaration: pentameric(5) Consistent with protein copy count Chain 7; UniProt 1–417 Not recorded Capsid protein VP1 × 1 (P03300) Capsid protein VP2 × 1 (P03300) Capsid protein VP3 × 1 (P03300) Capsid protein VP4 × 1 (P03300) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:PBS;pH 7;PBS cryo-EM vitrification conditions:Sample mixed and frozen within 2 minutes.;120 K;Cryogen ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. Resolution 3.70 Å
3 Other combination Heteromer Protein × 25 其他Polymer 30 PDB declaration: 25-meric(25) Consistent with protein copy count Chain 7; UniProt 1–417 Not recorded Capsid protein VP1 × 5 (P03300) Capsid protein VP2 × 5 (P03300) Capsid protein VP3 × 5 (P03300) Capsid protein VP4 × 5 (P03300) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 5 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY cryo-EM buffer:PBS;pH 7;PBS cryo-EM vitrification conditions:Sample mixed and frozen within 2 minutes.;120 K;Cryogen ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. Resolution 3.70 Å
4 Other combination Heteromer Protein × 30 其他Polymer 36 PDB declaration: 30-meric(30) Consistent with protein copy count Chain 7; UniProt 1–417 Not recorded Capsid protein VP1 × 6 (P03300) Capsid protein VP2 × 6 (P03300) Capsid protein VP3 × 6 (P03300) Capsid protein VP4 × 6 (P03300) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 6 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM buffer:PBS;pH 7;PBS cryo-EM vitrification conditions:Sample mixed and frozen within 2 minutes.;120 K;Cryogen ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. Resolution 3.70 Å
5 Other combination Heteromer Protein × 5 其他Polymer 6 PDB declaration: pentameric(5) Consistent with protein copy count Chain 7; UniProt 1–417 Not recorded Capsid protein VP1 × 1 (P03300) Capsid protein VP2 × 1 (P03300) Capsid protein VP3 × 1 (P03300) Capsid protein VP4 × 1 (P03300) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:PBS;pH 7;PBS cryo-EM vitrification conditions:Sample mixed and frozen within 2 minutes.;120 K;Cryogen ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. Resolution 3.70 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 5
Chains and sequence ranges Author chain 7; PDBConstruct 1–417; UniProt 1–417

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 3j8f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3j8f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3j8f
Deposition date deposition_date2014-10-20
Structure title titleCryo-EM reconstruction of poliovirus-receptor complex
Keywords keywordspoliovirus, receptor, PVR, CD155, VIRUS-SIGNALING PROTEIN complex; VIRUS/SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier41.33
Radius of gyration Rg (electron density) rg_electron41.99
Forward intensity I(0) i0267914000.00
Molecular weight molecular_weight131720.0 kDa
Excluded volume excluded_volume164550 ų
Envelope volume envelope_volume235820 ų
Hydration-shell volume shell_volume50826 ų
Envelope diameter envelope_diameter166.6
Shell Rg shell_rg42.61
Envelope Rg envelope_rg44.83
Shape Rg shape_rg41.96
Total Rg total_rg42.11
Total atoms total_atoms9263
Residues n_residues1159
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 dmax156.0
Rg (real space) rg_real42.08
Rg uncertainty (real space) rg_real_error1.98
I(0) (real space) i0_real2.6790e+08
I(0) uncertainty (real space) i0_real_error5.1560e+06
Rg (reciprocal space) rg_reciprocal41.34
I(0) (reciprocal space) i0_reciprocal267700000.0000
Solution quality estimate total_estimate0.7286
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.0
Skewness Skewness skewness0.936
Kurtosis Kurtosis kurtosis0.558
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25210000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.347; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.774; Smooth: 0.653

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id3j8f100
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id3j8f200
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id3j8f300
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id3j8f400
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily10 — Picornavirus coat protein VP4
Domain ID domain_id3j8f701
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3j8f702
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3j8f703
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)