7b5f

Structure of echovirus 18 in complex with neonatal Fc receptor

Method: ELECTRON MICROSCOPY Dmax: 103.3 Å Quality: GOOD

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

Echovirus 18 viral protein 3

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 heterocomplex Heteromer Protein × 6 PDB declaration: Hexameric(6) Consistent with protein copy count Chain A; UniProt 569–855 Chain B; UniProt 70–329 Chain C; UniProt 330–568 Chain D; UniProt 1–69 Not recorded IgG receptor FcRn large subunit p51 × 1 (P55899) Beta-2-microglobulin × 1 (P61769) 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

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.

6 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8V635_9ENTO
Isoform
PDB entities 1, 2, 3, 4
Chains and sequence ranges Author chain C; PDBConstruct 1–239; UniProt 330–568 Author chain D; PDBConstruct 1–69; UniProt 1–69 Author chain A; PDBConstruct 1–287; UniProt 569–855 Author chain B; PDBConstruct 1–260; UniProt 70–329

IgG receptor FcRn large subunit p51

Homo sapiens

UniProt P55899

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 × 6 PDB declaration: Hexameric(6) Consistent with protein copy count Chain G; UniProt 24–290 Not recorded Echovirus 18 viral protein 3 × 1 (Q8V635) Echovirus 18 viral protein 4 × 1 (Q8V635) Echovirus 18 viral protein 1 × 1 (Q8V635) Echovirus 18 viral protein 2 × 1 (Q8V635) Beta-2-microglobulin × 1 (P61769) 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

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.

30 other PDB entries and 70 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FCGRN_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain G; PDBConstruct 1–267; UniProt 24–290

Beta-2-microglobulin

Homo sapiens

UniProt P61769

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 × 6 PDB declaration: Hexameric(6) Consistent with protein copy count Chain H; UniProt 21–119 Not recorded Echovirus 18 viral protein 3 × 1 (Q8V635) Echovirus 18 viral protein 4 × 1 (Q8V635) Echovirus 18 viral protein 1 × 1 (Q8V635) Echovirus 18 viral protein 2 × 1 (Q8V635) IgG receptor FcRn large subunit p51 × 1 (P55899) 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

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.

1313 other PDB entries and 1998 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B2MG_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain H; PDBConstruct 1–99; UniProt 21–119

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 7b5f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7b5f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7b5f
Deposition date deposition_date2020-12-03
Structure title titleStructure of echovirus 18 in complex with neonatal Fc receptor
Keywords keywordscomplex, echovirus 18 virion, neonatal fc receptor, fcrn, beta-2-microglobulin, microglobulin, pocket factor, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier31.28
Radius of gyration Rg (electron density) rg_electron30.62
Forward intensity I(0) i0175629000.00
Molecular weight molecular_weight106110.0 kDa
Excluded volume excluded_volume132650 ų
Envelope volume envelope_volume160980 ų
Hydration-shell volume shell_volume42953 ų
Envelope diameter envelope_diameter110.2
Shell Rg shell_rg38.46
Envelope Rg envelope_rg31.31
Shape Rg shape_rg30.63
Total Rg total_rg31.19
Total atoms total_atoms7471
Residues n_residues958
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 dmax103.3
Rg (real space) rg_real31.25
Rg uncertainty (real space) rg_real_error0.74
I(0) (real space) i0_real1.7560e+08
I(0) uncertainty (real space) i0_real_error2.8080e+06
Rg (reciprocal space) rg_reciprocal31.27
I(0) (reciprocal space) i0_reciprocal175600000.0000
Solution quality estimate total_estimate0.8893
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.5
Skewness Skewness skewness0.338
Kurtosis Kurtosis kurtosis-0.348
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha31330000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.973

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7b5fB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id7b5fG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like

8. Citations (1)

9. Files and Curves (10)