6la6

Cryo-EM structure of echovirus 11 complexed with its uncoating receptor FcRn at pH 7.4

Method: ELECTRON MICROSCOPY Dmax: 136.4 Å Quality: GOOD

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

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 × 360 PDB declaration: 360-meric(360) Consistent with protein copy count Chain E; UniProt 28–290 Not recorded Capsid protein VP1 × 60 Capsid protein VP2 × 60 Capsid protein VP3 × 60 Capsid protein VP4 × 60 Beta-2-microglobulin × 60 (P61769) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.39 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 28–290 Not recorded Capsid protein VP1 × 1 Capsid protein VP2 × 1 Capsid protein VP3 × 1 Capsid protein VP4 × 1 Beta-2-microglobulin × 1 (P61769) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.39 Å
3 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain E; UniProt 28–290 Not recorded Capsid protein VP1 × 5 Capsid protein VP2 × 5 Capsid protein VP3 × 5 Capsid protein VP4 × 5 Beta-2-microglobulin × 5 (P61769) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.39 Å
4 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain E; UniProt 28–290 Not recorded Capsid protein VP1 × 6 Capsid protein VP2 × 6 Capsid protein VP3 × 6 Capsid protein VP4 × 6 Beta-2-microglobulin × 6 (P61769) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.39 Å
5 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 28–290 Not recorded Capsid protein VP1 × 1 Capsid protein VP2 × 1 Capsid protein VP3 × 1 Capsid protein VP4 × 1 Beta-2-microglobulin × 1 (P61769) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.39 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.

30 other PDB entries and 66 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 E; PDBConstruct 1–263; UniProt 28–290

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 × 360 PDB declaration: 360-meric(360) Consistent with protein copy count Chain F; UniProt 21–119 Not recorded Capsid protein VP1 × 60 Capsid protein VP2 × 60 Capsid protein VP3 × 60 Capsid protein VP4 × 60 IgG receptor FcRn large subunit p51 × 60 (P55899) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.39 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain F; UniProt 21–119 Not recorded Capsid protein VP1 × 1 Capsid protein VP2 × 1 Capsid protein VP3 × 1 Capsid protein VP4 × 1 IgG receptor FcRn large subunit p51 × 1 (P55899) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.39 Å
3 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain F; UniProt 21–119 Not recorded Capsid protein VP1 × 5 Capsid protein VP2 × 5 Capsid protein VP3 × 5 Capsid protein VP4 × 5 IgG receptor FcRn large subunit p51 × 5 (P55899) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.39 Å
4 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain F; UniProt 21–119 Not recorded Capsid protein VP1 × 6 Capsid protein VP2 × 6 Capsid protein VP3 × 6 Capsid protein VP4 × 6 IgG receptor FcRn large subunit p51 × 6 (P55899) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.39 Å
5 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain F; UniProt 21–119 Not recorded Capsid protein VP1 × 1 Capsid protein VP2 × 1 Capsid protein VP3 × 1 Capsid protein VP4 × 1 IgG receptor FcRn large subunit p51 × 1 (P55899) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.39 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.

1313 other PDB entries and 1994 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 F; 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 6la6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6la6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6la6
Deposition date deposition_date2019-11-12
Structure title titleCryo-EM structure of echovirus 11 complexed with its uncoating receptor FcRn at pH 7.4
Keywords keywordsCryo-EM structure, echovirus 11, FcRn, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier39.10
Radius of gyration Rg (electron density) rg_electron38.91
Forward intensity I(0) i0277610000.00
Molecular weight molecular_weight133680.0 kDa
Excluded volume excluded_volume166490 ų
Envelope volume envelope_volume230910 ų
Hydration-shell volume shell_volume50530 ų
Envelope diameter envelope_diameter139.4
Shell Rg shell_rg43.04
Envelope Rg envelope_rg39.48
Shape Rg shape_rg38.89
Total Rg total_rg39.24
Total atoms total_atoms9413
Residues n_residues1195
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 dmax136.4
Rg (real space) rg_real39.37
Rg uncertainty (real space) rg_real_error1.15
I(0) (real space) i0_real2.7760e+08
I(0) uncertainty (real space) i0_real_error5.0790e+06
Rg (reciprocal space) rg_reciprocal39.21
I(0) (reciprocal space) i0_reciprocal277600000.0000
Solution quality estimate total_estimate0.8496
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.5
Skewness Skewness skewness0.485
Kurtosis Kurtosis kurtosis-0.303
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha48120000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.827

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd6la6a_
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)
Domain ID domain_idd6la6c_
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)
Domain ID domain_idd6la6e1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd6la6e2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6la6f_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

8. Citations (1)

9. Files and Curves (10)