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6hbj

Echovirus 18 empty particle

Method: ELECTRON MICROSCOPY Dmax: 93.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Viral protein 1

OrganismNot specified

UniProt Q8V635

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 × 180 PDB declaration: 180-meric（180） Consistent with protein copy count Chain A； UniProt 569–855 Chain B； UniProt 70–329 Chain C； UniProt 330–568 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 5.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.16 Å R-free 0.336
2 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 569–855 Chain B； UniProt 70–329 Chain C； UniProt 330–568 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 5.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.16 Å R-free 0.336
3 Protein homooligomer Homooligomer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain A； UniProt 569–855 Chain B； UniProt 70–329 Chain C； UniProt 330–568 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 5.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.16 Å R-free 0.336
4 Protein homooligomer Homooligomer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count Chain A； UniProt 569–855 Chain B； UniProt 70–329 Chain C； UniProt 330–568 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 5.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.16 Å R-free 0.336
5 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 569–855 Chain B； UniProt 70–329 Chain C； UniProt 330–568 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 5.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.16 Å R-free 0.336

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 6HBJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6HBG Echovirus 18 native particle Deposited 2018-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 569–855（287 aa）
Chain B 70–329（260 aa）
Chain C 330–568（239 aa）
Chain D 1–69（69 aa）
Not recorded PLM PALMITIC ACID × 60 GUN GUANINE × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å R-free 0.325
6HBH Echovirus 18 A-particle Deposited 2018-08-10 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric
Chain A 569–855（287 aa）
Chain B 70–329（260 aa）
Chain C 330–568（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å R-free 0.323
6HBH Echovirus 18 A-particle Deposited 2018-08-10 Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 569–855（287 aa）
Chain B 70–329（260 aa）
Chain C 330–568（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å R-free 0.323
6HBH Echovirus 18 A-particle Deposited 2018-08-10 Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 569–855（287 aa）
Chain B 70–329（260 aa）
Chain C 330–568（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å R-free 0.323
6HBH Echovirus 18 A-particle Deposited 2018-08-10 Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain A 569–855（287 aa）
Chain B 70–329（260 aa）
Chain C 330–568（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å R-free 0.323
6HBH Echovirus 18 A-particle Deposited 2018-08-10 Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 569–855（287 aa）
Chain B 70–329（260 aa）
Chain C 330–568（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å R-free 0.323
6HBK Echovirus 18 Open particle without one pentamer Deposited 2018-08-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 165 PDB declaration: 165-meric
Chain A 569–855（287 aa）
Chain B 70–328（259 aa）
Chain C 330–568（239 aa）
Chain D 569–855（287 aa）
Chain E 70–328（259 aa）
Chain F 330–568（239 aa）
Chain G 569–855（287 aa）
Chain H 70–328（259 aa）
Chain I 330–568（239 aa）
Chain J 569–855（287 aa）
Chain K 70–328（259 aa）
Chain L 330–568（239 aa）
Chain M 569–855（287 aa）
Chain N 70–328（259 aa）
Chain O 330–568（239 aa）
Chain P 569–855（287 aa）
Chain Q 70–328（259 aa）
Chain R 330–568（239 aa）
Chain S 569–855（287 aa）
Chain T 70–328（259 aa）
Chain U 330–568（239 aa）
Chain V 569–855（287 aa）
Chain W 70–328（259 aa）
Chain X 330–568（239 aa）
Chain Y 569–855（287 aa）
Chain Z 70–328（259 aa）
Chain a 330–568（239 aa）
Chain b 569–855（287 aa）
Chain c 70–328（259 aa）
Chain d 330–568（239 aa）
Chain e 569–855（287 aa）
Chain f 70–328（259 aa）
Chain g 330–568（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6HBL Echovirus 18 Open particle without three pentamers Deposited 2018-08-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 135 PDB declaration: 45-meric
Chain A 569–855（287 aa）
Chain B 70–329（260 aa）
Chain C 330–568（239 aa）
Chain D 569–855（287 aa）
Chain E 70–329（260 aa）
Chain F 330–568（239 aa）
Chain G 569–855（287 aa）
Chain H 70–329（260 aa）
Chain I 330–568（239 aa）
Chain J 569–855（287 aa）
Chain K 70–329（260 aa）
Chain L 330–568（239 aa）
Chain M 569–855（287 aa）
Chain N 70–329（260 aa）
Chain O 330–568（239 aa）
Chain P 569–855（287 aa）
Chain Q 70–329（260 aa）
Chain R 330–568（239 aa）
Chain S 569–855（287 aa）
Chain T 70–329（260 aa）
Chain U 330–568（239 aa）
Chain V 569–855（287 aa）
Chain W 70–329（260 aa）
Chain X 330–568（239 aa）
Chain Y 569–855（287 aa）
Chain Z 70–329（260 aa）
Chain a 330–568（239 aa）
Chain b 569–855（287 aa）
Chain c 70–329（260 aa）
Chain d 330–568（239 aa）
Chain e 569–855（287 aa）
Chain f 70–329（260 aa）
Chain g 330–568（239 aa）
Chain h 569–855（287 aa）
Chain i 70–329（260 aa）
Chain j 330–568（239 aa）
Chain k 569–855（287 aa）
Chain l 70–329（260 aa）
Chain m 330–568（239 aa）
Chain n 569–855（287 aa）
Chain o 70–329（260 aa）
Chain p 330–568（239 aa）
Chain q 569–855（287 aa）
Chain r 70–329（260 aa）
Chain s 330–568（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6HHT Echovirus 18 Open particle without two pentamers Deposited 2018-08-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 150 PDB declaration: 150-meric
Chain A1 569–855（287 aa）
Chain A2 569–855（287 aa）
Chain B1 70–329（260 aa）
Chain B2 70–329（260 aa）
Chain C1 330–568（239 aa）
Chain C2 330–568（239 aa）
Chain D1 569–855（287 aa）
Chain D2 569–855（287 aa）
Chain E1 70–329（260 aa）
Chain E2 70–329（260 aa）
Chain F1 330–568（239 aa）
Chain F2 330–568（239 aa）
Chain G1 569–855（287 aa）
Chain G2 569–855（287 aa）
Chain H1 70–329（260 aa）
Chain H2 70–329（260 aa）
Chain I1 330–568（239 aa）
Chain I2 330–568（239 aa）
Chain J1 569–855（287 aa）
Chain J2 569–855（287 aa）
Chain K1 70–329（260 aa）
Chain K2 70–329（260 aa）
Chain L1 330–568（239 aa）
Chain L2 330–568（239 aa）
Chain M1 569–855（287 aa）
Chain M2 569–855（287 aa）
Chain N1 70–329（260 aa）
Chain N2 70–329（260 aa）
Chain O1 330–568（239 aa）
Chain O2 330–568（239 aa）
Chain P1 569–855（287 aa）
Chain P2 569–855（287 aa）
Chain Q1 70–329（260 aa）
Chain Q2 70–329（260 aa）
Chain R1 330–568（239 aa）
Chain R2 330–568（239 aa）
Chain S1 569–855（287 aa）
Chain S2 569–855（287 aa）
Chain T1 70–329（260 aa）
Chain T2 70–329（260 aa）
Chain U1 330–568（239 aa）
Chain U2 330–568（239 aa）
Chain V1 569–855（287 aa）
Chain V2 569–855（287 aa）
Chain W1 70–329（260 aa）
Chain W2 70–329（260 aa）
Chain X1 330–568（239 aa）
Chain X2 330–568（239 aa）
Chain Y2 569–855（287 aa）
Chain Z2 70–329（260 aa）
Chain a2 330–568（239 aa）
Chain b2 569–855（287 aa）
Chain c2 70–329（260 aa）
Chain d2 330–568（239 aa）
Chain e2 569–855（287 aa）
Chain f2 70–329（260 aa）
Chain g2 330–568（239 aa）
Chain h2 569–855（287 aa）
Chain i2 70–329（260 aa）
Chain j2 330–568（239 aa）
Chain k2 569–855（287 aa）
Chain l2 70–329（260 aa）
Chain m2 330–568（239 aa）
Chain n2 569–855（287 aa）
Chain o2 70–329（260 aa）
Chain p2 330–568（239 aa）
Chain q2 569–855（287 aa）
Chain r2 70–329（260 aa）
Chain s2 330–568（239 aa）
Chain t2 569–855（287 aa）
Chain u2 70–329（260 aa）
Chain v2 330–568（239 aa）
Chain w2 569–855（287 aa）
Chain x2 70–329（260 aa）
Chain y2 330–568（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
7B5F Structure of echovirus 18 in complex with neonatal Fc receptor Deposited 2020-12-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: Hexameric
Chain A 569–855（287 aa）
Chain B 70–329（260 aa）
Chain C 330–568（239 aa）
Chain D 1–69（69 aa）
Not recorded PLM PALMITIC ACID × 1 GUN GUANINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3；Mixed in 1:1 volume ratio {20 mM Tris (pH=7.2), 100 mM NaCl} and {8 mM Na2HPO4, 2 mM KH2PO4 (pH=7.4), 137 mM NaCl, 2.7 mM KCl}=PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å R-free 0.311

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8V635_9ENTO
Isoform —
PDB entities 1, 2, 3
Chains and sequence ranges Author chain A； PDBConstruct 1–287； UniProt 569–855 Author chain B； PDBConstruct 1–260； UniProt 70–329 Author chain C； PDBConstruct 1–239； UniProt 330–568

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 6hbj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6hbj
Deposition date deposition_date2018-08-10
Structure title titleEchovirus 18 empty particle
Keywords keywordsechovirus, echovirus 18, empty particle, B-particle, enterovirus, picornavirus, 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_guinier28.62 Å
Radius of gyration Rg (electron density) rg_electron27.91 Å
Forward intensity I(0) i079084500.00
Molecular weight molecular_weight71371.0 kDa
Excluded volume excluded_volume89796 ų
Envelope volume envelope_volume110750 ų
Hydration-shell volume shell_volume33528 ų
Envelope diameter envelope_diameter101.7 Å
Shell Rg shell_rg34.86 Å
Envelope Rg envelope_rg28.58 Å
Shape Rg shape_rg27.90 Å
Total Rg total_rg28.59 Å
Total atoms total_atoms5016
Residues n_residues661
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 dmax93.8 Å
Rg (real space) rg_real28.65 Å
Rg uncertainty (real space) rg_real_error0.72 Å
I(0) (real space) i0_real7.9080e+07
I(0) uncertainty (real space) i0_real_error1.1280e+06
Rg (reciprocal space) rg_reciprocal28.64 Å
I(0) (reciprocal space) i0_reciprocal79080000.0000
Solution quality estimate total_estimate0.8834
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.4 Å
Skewness Skewness skewness0.411
Kurtosis Kurtosis kurtosis-0.258
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17800000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.881
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6hbjc_
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)

CATH v4.4 (3 domains)

Domain ID domain_id6hbjA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id6hbjB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id6hbjC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)