2h2r

Crystal structure of the human CD23 Lectin domain, apo form

Method: X-RAY DIFFRACTION Dmax: 88.9 Å Quality: GOOD

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

;Low affinity immunoglobulin epsilon Fc receptor (Lymphocyte IgE receptor) (Fc-epsilon-RII)(Immunoglobulin E-binding factor) (CD23 antigen) ;

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 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 150–321 Chain B; UniProt 150–321 Fragment:lectin domain Mutation:H213R, G256S No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.2;293 K;1.2 M sodium monobasic phosphate, 0.8 M potassium dibasic phosphate, 0.1 M Caps buffer pH 10.5, and 0.2 M lithium sulfate; final pH 6.2 , VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.50 Å R-free 0.165

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 79 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FCER2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–175; UniProt 150–321 Author chain B; PDBConstruct 4–175; UniProt 150–321

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 2h2r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2h2r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2h2r
Deposition date deposition_date2006-05-19
Structure title titleCrystal structure of the human CD23 Lectin domain, apo form
Keywords keywordsC-type lectin, apo form, lectin domain, low affinity IgE 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_guinier24.32
Radius of gyration Rg (electron density) rg_electron24.08
Forward intensity I(0) i018117600.00
Molecular weight molecular_weight30872.0 kDa
Excluded volume excluded_volume37825 ų
Envelope volume envelope_volume46472 ų
Hydration-shell volume shell_volume17209 ų
Envelope diameter envelope_diameter93.6
Shell Rg shell_rg29.19
Envelope Rg envelope_rg24.21
Shape Rg shape_rg24.07
Total Rg total_rg24.73
Total atoms total_atoms2167
Residues n_residues269
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 dmax88.9
Rg (real space) rg_real24.58
Rg uncertainty (real space) rg_real_error0.81
I(0) (real space) i0_real1.8120e+07
I(0) uncertainty (real space) i0_real_error2.4390e+05
Rg (reciprocal space) rg_reciprocal24.53
I(0) (reciprocal space) i0_reciprocal18120000.0000
Solution quality estimate total_estimate0.7619
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.2
Skewness Skewness skewness0.492
Kurtosis Kurtosis kurtosis-0.386
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3226000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.542; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.344; Smooth: 0.928

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2h2ra_
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_idd2h2rb_
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 (2 domains)

Domain ID domain_id2h2rA01
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_id2h2rB01
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)