1xed

Crystal Structure of a Ligand-Binding Domain of the Human Polymeric Ig Receptor, pIgR

Method: X-RAY DIFFRACTION Dmax: 107.2 Å Quality: GOOD

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

Polymeric-immunoglobulin receptor

Homo sapiens

UniProt P01833

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 19–127 Fragment:N-Terminal Domain I MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;293 K;PEG 8000, Magnesium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50 Resolution 1.90 Å R-free 0.244
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 19–127 Fragment:N-Terminal Domain I MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;293 K;PEG 8000, Magnesium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50 Resolution 1.90 Å R-free 0.244
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 19–127 Fragment:N-Terminal Domain I No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;293 K;PEG 8000, Magnesium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50 Resolution 1.90 Å R-free 0.244
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 19–127 Fragment:N-Terminal Domain I No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;293 K;PEG 8000, Magnesium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50 Resolution 1.90 Å R-free 0.244
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 19–127 Fragment:N-Terminal Domain I No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;293 K;PEG 8000, Magnesium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50 Resolution 1.90 Å R-free 0.244
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain F; UniProt 19–127 Fragment:N-Terminal Domain I No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;293 K;PEG 8000, Magnesium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50 Resolution 1.90 Å R-free 0.244
7 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 19–127 Chain B; UniProt 19–127 Chain C; UniProt 19–127 Chain D; UniProt 19–127 Fragment:N-Terminal Domain I MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;293 K;PEG 8000, Magnesium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50 Resolution 1.90 Å R-free 0.244
8 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 19–127 Chain D; UniProt 19–127 Fragment:N-Terminal Domain I MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;293 K;PEG 8000, Magnesium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50 Resolution 1.90 Å R-free 0.244
9 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 19–127 Chain C; UniProt 19–127 Fragment:N-Terminal Domain I MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;293 K;PEG 8000, Magnesium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50 Resolution 1.90 Å R-free 0.244

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.

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PIGR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–109; UniProt 19–127 Author chain B; PDBConstruct 1–109; UniProt 19–127 Author chain C; PDBConstruct 1–109; UniProt 19–127 Author chain D; PDBConstruct 1–109; UniProt 19–127 Author chain E; PDBConstruct 1–109; UniProt 19–127 Author chain F; PDBConstruct 1–109; UniProt 19–127

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 1xed

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1xed
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1xed
Deposition date deposition_date2004-09-10
Structure title titleCrystal Structure of a Ligand-Binding Domain of the Human Polymeric Ig Receptor, pIgR
Keywords keywordsIg-like fold, 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_guinier30.73
Radius of gyration Rg (electron density) rg_electron30.42
Forward intensity I(0) i087142500.00
Molecular weight molecular_weight70857.0 kDa
Excluded volume excluded_volume87249 ų
Envelope volume envelope_volume109270 ų
Hydration-shell volume shell_volume31705 ų
Envelope diameter envelope_diameter112.8
Shell Rg shell_rg35.49
Envelope Rg envelope_rg30.70
Shape Rg shape_rg30.43
Total Rg total_rg30.84
Total atoms total_atoms4990
Residues n_residues652
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 dmax107.2
Rg (real space) rg_real31.00
Rg uncertainty (real space) rg_real_error1.01
I(0) (real space) i0_real8.7140e+07
I(0) uncertainty (real space) i0_real_error1.3830e+06
Rg (reciprocal space) rg_reciprocal30.88
I(0) (reciprocal space) i0_reciprocal87130000.0000
Solution quality estimate total_estimate0.8245
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.9
Skewness Skewness skewness0.571
Kurtosis Kurtosis kurtosis-0.229
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10600000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.668; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.799; Smooth: 0.913

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1xeda1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd1xeda2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1xedb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd1xedb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1xedc1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd1xedc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1xedd1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd1xedd2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1xede1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd1xede2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1xedf1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd1xedf2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id1xedA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1xedB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1xedC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1xedD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1xedE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1xedF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)