4ezm

Crystal structure of the human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23

Method: X-RAY DIFFRACTION Dmax: 182.4 Å Quality: REASONABLE

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

Ig epsilon chain C region

Homo sapiens

UniProt P01854

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 × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 209–428 Chain B; UniProt 209–428 Fragment:Human IgE-Fc(epsilon)3-4, UNP residues 209-428 Low affinity immunoglobulin epsilon Fc receptor × 2 (P06734) ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;298 K;3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K Resolution 3.10 Å R-free 0.283
2 Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 209–428 Chain D; UniProt 209–428 Fragment:Human IgE-Fc(epsilon)3-4, UNP residues 209-428 Low affinity immunoglobulin epsilon Fc receptor × 2 (P06734) ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 MAN alpha-D-mannopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;298 K;3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K Resolution 3.10 Å R-free 0.283
3 Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 209–428 Chain F; UniProt 209–428 Fragment:Human IgE-Fc(epsilon)3-4, UNP residues 209-428 Low affinity immunoglobulin epsilon Fc receptor × 2 (P06734) ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;298 K;3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K Resolution 3.10 Å R-free 0.283

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.

33 other PDB entries and 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IGHE_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–223; UniProt 209–428 Author chain B; PDBConstruct 4–223; UniProt 209–428 Author chain C; PDBConstruct 4–223; UniProt 209–428 Author chain D; PDBConstruct 4–223; UniProt 209–428 Author chain E; PDBConstruct 4–223; UniProt 209–428 Author chain F; PDBConstruct 4–223; UniProt 209–428

Low affinity immunoglobulin epsilon Fc receptor

Homo sapiens

UniProt P06734

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 × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 156–298 Chain H; UniProt 156–298 Fragment:Human derCD23, UNP residues 156-298 Ig epsilon chain C region × 2 (P01854) ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;298 K;3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K Resolution 3.10 Å R-free 0.283
2 Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain I; UniProt 156–298 Chain J; UniProt 156–298 Fragment:Human derCD23, UNP residues 156-298 Ig epsilon chain C region × 2 (P01854) ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 MAN alpha-D-mannopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;298 K;3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K Resolution 3.10 Å R-free 0.283
3 Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric(4) Consistent with protein copy count Chain K; UniProt 156–298 Chain L; UniProt 156–298 Fragment:Human derCD23, UNP residues 156-298 Ig epsilon chain C region × 2 (P01854) ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;298 K;3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K Resolution 3.10 Å R-free 0.283

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.

22 other PDB entries and 77 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FCER2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain G; PDBConstruct 1–143; UniProt 156–298 Author chain H; PDBConstruct 1–143; UniProt 156–298 Author chain I; PDBConstruct 1–143; UniProt 156–298 Author chain J; PDBConstruct 1–143; UniProt 156–298 Author chain K; PDBConstruct 1–143; UniProt 156–298 Author chain L; PDBConstruct 1–143; UniProt 156–298

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 4ezm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ezm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ezm
Deposition date deposition_date2012-05-03
Structure title titleCrystal structure of the human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23
Keywords keywordsImmunoglobulin fold Lectin, Antibody Receptor, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier54.06
Radius of gyration Rg (electron density) rg_electron53.91
Forward intensity I(0) i0854995000.00
Molecular weight molecular_weight234590.0 kDa
Excluded volume excluded_volume290040 ų
Envelope volume envelope_volume469390 ų
Hydration-shell volume shell_volume75212 ų
Envelope diameter envelope_diameter190.4
Shell Rg shell_rg54.71
Envelope Rg envelope_rg51.90
Shape Rg shape_rg53.90
Total Rg total_rg53.94
Total atoms total_atoms16492
Residues n_residues2022
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 dmax182.4
Rg (real space) rg_real54.02
Rg uncertainty (real space) rg_real_error1.98
I(0) (real space) i0_real8.5500e+08
I(0) uncertainty (real space) i0_real_error2.0560e+07
Rg (reciprocal space) rg_reciprocal54.08
I(0) (reciprocal space) i0_reciprocal855100000.0000
Solution quality estimate total_estimate0.6474
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary69.2
Skewness Skewness skewness0.239
Kurtosis Kurtosis kurtosis-0.334
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26030000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 0.017; Positv: 1.000; Valcen: 0.997; Smooth: 0.774

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

Domain ID domain_idd4ezma1
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_idd4ezma2
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_idd4ezmb1
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_idd4ezmb2
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_idd4ezmc1
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_idd4ezmc2
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_idd4ezmd1
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_idd4ezmd2
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_idd4ezme1
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_idd4ezme2
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_idd4ezmf1
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_idd4ezmf2
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_idd4ezmg_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd4ezmh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd4ezmi_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd4ezmj_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd4ezmk_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd4ezml_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain

CATH v4.4 (18 domains)

Domain ID domain_id4ezmA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ezmA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ezmB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ezmB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ezmC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ezmC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ezmD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ezmD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ezmE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ezmE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ezmF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ezmF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ezmG01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id4ezmH01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id4ezmI01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id4ezmJ01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id4ezmK01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id4ezmL01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A

8. Citations (1)

9. Files and Curves (10)