3j9f

Poliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C

Method: ELECTRON MICROSCOPY Dmax: 154.3 Å Quality: REASONABLE

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

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 × 420 其他Polymer 360 PDB declaration: 420-meric(420) 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) Poliovirus receptor × 60 (P15151) 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 ;alpha-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 PLM PALMITIC ACID × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 60 ELECTRON MICROSCOPY cryo-EM vitrification conditions:Cryogen ETHANE Resolution 9.00 Å
2 Other combination Heteromer Protein × 7 其他Polymer 6 PDB declaration: heptameric(7) 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) Poliovirus receptor × 1 (P15151) 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 ;alpha-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 PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM vitrification conditions:Cryogen ETHANE Resolution 9.00 Å
3 Other combination Heteromer Protein × 35 其他Polymer 30 PDB declaration: 35-meric(35) 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) Poliovirus receptor × 5 (P15151) 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 ;alpha-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 PLM PALMITIC ACID × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY cryo-EM vitrification conditions:Cryogen ETHANE Resolution 9.00 Å
4 Other combination Heteromer Protein × 42 其他Polymer 36 PDB declaration: 42-meric(42) 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) Poliovirus receptor × 6 (P15151) 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 ;alpha-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 PLM PALMITIC ACID × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM vitrification conditions:Cryogen ETHANE Resolution 9.00 Å
5 Other combination Heteromer Protein × 7 其他Polymer 6 PDB declaration: heptameric(7) 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) Poliovirus receptor × 1 (P15151) 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 ;alpha-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 PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM vitrification conditions:Cryogen ETHANE Resolution 9.00 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 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

OrganismNot specified

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 × 420 其他Polymer 360 PDB declaration: 420-meric(420) Consistent with protein copy count Chain 7; UniProt 28–143 Chain 8; UniProt 142–243 Chain 9; UniProt 242–333 Fragment:SEE REMARK 999 Protein VP1 × 60 (P03300) Protein VP2 × 60 (P03300) Protein VP3 × 60 (P03300) 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 ;alpha-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 PLM PALMITIC ACID × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 60 ELECTRON MICROSCOPY cryo-EM vitrification conditions:Cryogen ETHANE Resolution 9.00 Å
2 Other combination Heteromer Protein × 7 其他Polymer 6 PDB declaration: heptameric(7) Consistent with protein copy count Chain 7; UniProt 28–143 Chain 8; UniProt 142–243 Chain 9; UniProt 242–333 Fragment:SEE REMARK 999 Protein VP1 × 1 (P03300) Protein VP2 × 1 (P03300) Protein VP3 × 1 (P03300) 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 ;alpha-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 PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM vitrification conditions:Cryogen ETHANE Resolution 9.00 Å
3 Other combination Heteromer Protein × 35 其他Polymer 30 PDB declaration: 35-meric(35) Consistent with protein copy count Chain 7; UniProt 28–143 Chain 8; UniProt 142–243 Chain 9; UniProt 242–333 Fragment:SEE REMARK 999 Protein VP1 × 5 (P03300) Protein VP2 × 5 (P03300) Protein VP3 × 5 (P03300) 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 ;alpha-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 PLM PALMITIC ACID × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY cryo-EM vitrification conditions:Cryogen ETHANE Resolution 9.00 Å
4 Other combination Heteromer Protein × 42 其他Polymer 36 PDB declaration: 42-meric(42) Consistent with protein copy count Chain 7; UniProt 28–143 Chain 8; UniProt 142–243 Chain 9; UniProt 242–333 Fragment:SEE REMARK 999 Protein VP1 × 6 (P03300) Protein VP2 × 6 (P03300) Protein VP3 × 6 (P03300) 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 ;alpha-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 PLM PALMITIC ACID × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM vitrification conditions:Cryogen ETHANE Resolution 9.00 Å
5 Other combination Heteromer Protein × 7 其他Polymer 6 PDB declaration: heptameric(7) Consistent with protein copy count Chain 7; UniProt 28–143 Chain 8; UniProt 142–243 Chain 9; UniProt 242–333 Fragment:SEE REMARK 999 Protein VP1 × 1 (P03300) Protein VP2 × 1 (P03300) Protein VP3 × 1 (P03300) 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 ;alpha-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 PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM vitrification conditions:Cryogen ETHANE Resolution 9.00 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 5, 6, 7
Chains and sequence ranges Author chain 7; PDBConstruct 1–116; UniProt 28–143 Author chain 8; PDBConstruct 1–102; UniProt 142–243 Author chain 9; PDBConstruct 1–92; UniProt 242–333

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 3j9f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3j9f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3j9f
Deposition date deposition_date2015-01-15
Structure title titlePoliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C
Keywords keywordsdeglycosylated receptor, picornavirus, PVR, CD155, enterovirus, cell entry, VIRUS-CELL ADHESION complex; VIRUS/CELL ADHESION
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier40.59
Radius of gyration Rg (electron density) rg_electron41.12
Forward intensity I(0) i0267979000.00
Molecular weight molecular_weight131980.0 kDa
Excluded volume excluded_volume165000 ų
Envelope volume envelope_volume229830 ų
Hydration-shell volume shell_volume50332 ų
Envelope diameter envelope_diameter165.5
Shell Rg shell_rg42.22
Envelope Rg envelope_rg43.71
Shape Rg shape_rg41.09
Total Rg total_rg41.27
Total atoms total_atoms9281
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 dmax154.3
Rg (real space) rg_real41.26
Rg uncertainty (real space) rg_real_error1.77
I(0) (real space) i0_real2.6800e+08
I(0) uncertainty (real space) i0_real_error5.1500e+06
Rg (reciprocal space) rg_reciprocal40.60
I(0) (reciprocal space) i0_reciprocal267800000.0000
Solution quality estimate total_estimate0.7188
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.5
Skewness Skewness skewness0.928
Kurtosis Kurtosis kurtosis0.585
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25350000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.344; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.538; Smooth: 0.770

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (13)

8. Citations (1)

9. Files and Curves (10)