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6thd

Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E

Method: ELECTRON MICROSCOPY Dmax: 92.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Genome polyprotein

OrganismNot specified

UniProt P12915

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 homooligomer Homooligomer Protein × 240 PDB declaration: 240-meric（240） Consistent with protein copy count Chain 1； UniProt 560–840 Chain 2； UniProt 70–317 Chain 3； UniProt 318–559 Chain 4； UniProt 18–69 Not recorded MYR MYRISTIC ACID × 120 SO4 SULFATE ION × 120 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；PBS cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.23 Å
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain 1； UniProt 560–840 Chain 2； UniProt 70–317 Chain 3； UniProt 318–559 Chain 4； UniProt 18–69 Not recorded MYR MYRISTIC ACID × 2 SO4 SULFATE ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；PBS cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.23 Å
3 Protein homooligomer Homooligomer Protein × 20 PDB declaration: eicosameric（20） Consistent with protein copy count Chain 1； UniProt 560–840 Chain 2； UniProt 70–317 Chain 3； UniProt 318–559 Chain 4； UniProt 18–69 Not recorded MYR MYRISTIC ACID × 10 SO4 SULFATE ION × 10 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；PBS cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.23 Å
4 Protein homooligomer Homooligomer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain 1； UniProt 560–840 Chain 2； UniProt 70–317 Chain 3； UniProt 318–559 Chain 4； UniProt 18–69 Not recorded MYR MYRISTIC ACID × 12 SO4 SULFATE ION × 12 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；PBS cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.23 Å
5 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain 1； UniProt 560–840 Chain 2； UniProt 70–317 Chain 3； UniProt 318–559 Chain 4； UniProt 18–69 Not recorded MYR MYRISTIC ACID × 2 SO4 SULFATE ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；PBS cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.23 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.

Other PDB Difference from Current Entry 6THD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BEV BOVINE ENTEROVIRUS VG-5-27 Deposited 1996-04-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-MERIC
Chain 1 559–839（281 aa）
Chain 2 69–316（248 aa）
Chain 3 317–558（242 aa）
Chain 4 1–68（68 aa）
Not recorded SO4 SULFATE ION × 120 MYR MYRISTIC ACID × 60 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1BEV BOVINE ENTEROVIRUS VG-5-27 Deposited 1996-04-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain 1 559–839（281 aa）
Chain 2 69–316（248 aa）
Chain 3 317–558（242 aa）
Chain 4 1–68（68 aa）
Not recorded SO4 SULFATE ION × 2 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1BEV BOVINE ENTEROVIRUS VG-5-27 Deposited 1996-04-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 20 PDB declaration: eicosameric
Chain 1 559–839（281 aa）
Chain 2 69–316（248 aa）
Chain 3 317–558（242 aa）
Chain 4 1–68（68 aa）
Not recorded SO4 SULFATE ION × 10 MYR MYRISTIC ACID × 5 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1BEV BOVINE ENTEROVIRUS VG-5-27 Deposited 1996-04-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric
Chain 1 559–839（281 aa）
Chain 2 69–316（248 aa）
Chain 3 317–558（242 aa）
Chain 4 1–68（68 aa）
Not recorded SO4 SULFATE ION × 12 MYR MYRISTIC ACID × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1BEV BOVINE ENTEROVIRUS VG-5-27 Deposited 1996-04-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain 1 559–839（281 aa）
Chain 2 69–316（248 aa）
Chain 3 317–558（242 aa）
Chain 4 1–68（68 aa）
Not recorded SO4 SULFATE ION × 2 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1BEV BOVINE ENTEROVIRUS VG-5-27 Deposited 1996-04-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain 1 559–839（281 aa）
Chain 2 69–316（248 aa）
Chain 3 317–558（242 aa）
Chain 4 1–68（68 aa）
Not recorded SO4 SULFATE ION × 120 MYR MYRISTIC ACID × 60 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
6THN Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E symmetry expansion+2fold focused classification Deposited 2019-11-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 240 PDB declaration: 300-meric
Chain 1 560–840（281 aa）
Chain 2 70–317（248 aa）
Chain 3 318–559（242 aa）
Chain 4 18–69（52 aa）
Not recorded MYR MYRISTIC ACID × 120 SO4 SULFATE ION × 120 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6THN Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E symmetry expansion+2fold focused classification Deposited 2019-11-20 Different oligomeric state Different structure-quality metrics Assembly 2 Protein–RNA Homooligomer；Protein × 4 PDB declaration: pentameric
Chain 1 560–840（281 aa）
Chain 2 70–317（248 aa）
Chain 3 318–559（242 aa）
Chain 4 18–69（52 aa）
Not recorded MYR MYRISTIC ACID × 2 SO4 SULFATE ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6THN Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E symmetry expansion+2fold focused classification Deposited 2019-11-20 Different oligomeric state Different structure-quality metrics Assembly 3 Protein–RNA Homooligomer；Protein × 20 PDB declaration: 25-meric
Chain 1 560–840（281 aa）
Chain 2 70–317（248 aa）
Chain 3 318–559（242 aa）
Chain 4 18–69（52 aa）
Not recorded MYR MYRISTIC ACID × 10 SO4 SULFATE ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6THN Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E symmetry expansion+2fold focused classification Deposited 2019-11-20 Different oligomeric state Different structure-quality metrics Assembly 4 Protein–RNA Homooligomer；Protein × 24 PDB declaration: 30-meric
Chain 1 560–840（281 aa）
Chain 2 70–317（248 aa）
Chain 3 318–559（242 aa）
Chain 4 18–69（52 aa）
Not recorded MYR MYRISTIC ACID × 12 SO4 SULFATE ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6THN Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E symmetry expansion+2fold focused classification Deposited 2019-11-20 Different oligomeric state Different structure-quality metrics Assembly 5 Protein–RNA Homooligomer；Protein × 4 PDB declaration: pentameric
Chain 1 560–840（281 aa）
Chain 2 70–317（248 aa）
Chain 3 318–559（242 aa）
Chain 4 18–69（52 aa）
Not recorded MYR MYRISTIC ACID × 2 SO4 SULFATE ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å

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

View Construct and Data Evidence
UniProt name POLG_BOVEV
Isoform —
PDB entities 1, 2, 3, 4
Chains and sequence ranges Author chain 1； PDBConstruct 1–281； UniProt 560–840 Author chain 2； PDBConstruct 1–248； UniProt 70–317 Author chain 3； PDBConstruct 1–242； UniProt 318–559 Author chain 4； PDBConstruct 1–52； UniProt 18–69

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 6thd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6thd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6thd
Deposition date deposition_date2019-11-19
Structure title titleMultiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E
Keywords keywordsBEV1, enterovirus, picornavirus, RNA, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.12 Å
Radius of gyration Rg (electron density) rg_electron28.11 Å
Forward intensity I(0) i0131041000.00
Molecular weight molecular_weight90331.0 kDa
Excluded volume excluded_volume112790 ų
Envelope volume envelope_volume138060 ų
Hydration-shell volume shell_volume39720 ų
Envelope diameter envelope_diameter100.8 Å
Shell Rg shell_rg36.44 Å
Envelope Rg envelope_rg28.71 Å
Shape Rg shape_rg28.08 Å
Total Rg total_rg28.97 Å
Total atoms total_atoms6364
Residues n_residues812
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax92.5 Å
Rg (real space) rg_real29.04 Å
Rg uncertainty (real space) rg_real_error0.60 Å
I(0) (real space) i0_real1.3100e+08
I(0) uncertainty (real space) i0_real_error1.8520e+06
Rg (reciprocal space) rg_reciprocal29.07 Å
I(0) (reciprocal space) i0_reciprocal131000000.0000
Solution quality estimate total_estimate0.8977
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.3 Å
Skewness Skewness skewness0.281
Kurtosis Kurtosis kurtosis-0.367
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22420000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.957
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6thd1_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.0 — automated matches
Domain ID domain_idd6thd3_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)
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8. Citations (1)

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9. Files and Curves (10)