1adq

CRYSTAL STRUCTURE OF A HUMAN IGM RHEUMATOID FACTOR FAB IN COMPLEX WITH ITS AUTOANTIGEN IGG FC

Method: X-RAY DIFFRACTION Dmax: 120.0 Å Quality: GOOD

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

IGG4 REA FC

OrganismNot specified

UniProt P01861

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 118–323 Fragment:FC IGM-LAMBDA RF-AN FAB (LIGHT CHAIN) × 1 IGM-LAMBDA RF-AN FAB (HEAVY CHAIN) × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION. THE HANGING DROPS CONSISTED OF 2UL OF PROTEIN SOLUTION CONTAINING EACH PROTEIN AT 1MG/ML IN 0.1 % SODIUM AZIDE, 20MM TRIS-HCL AT PH 7.0, MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION TO BE SCREENED. CRYSTALS WERE OBTAINED WITH RESERVOIR SOLUTIONS CONTAINING 17.5 - 22.5 % (W/V) POLYETHYLENE GLYCOL (MEAN MW 8000) IN 0.1 % SODIUM AZIDE, 100MM TRIS-HCL, PH 7.0, AT TEMPERATURES BETWEEN 17.5 AND 21.5 (CELSIUS)., vapor diffusion - hanging drop Resolution 3.15 Å R-free 0.289

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.

13 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IGHG4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–206; UniProt 118–323

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 1adq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1adq
Deposition date deposition_date1997-02-18
Structure title titleCRYSTAL STRUCTURE OF A HUMAN IGM RHEUMATOID FACTOR FAB IN COMPLEX WITH ITS AUTOANTIGEN IGG FC
Keywords keywordsCOMPLEX (IMMUNOGLOBULIN-AUTOANTIGEN), RHEUMATOID FACTOR AUTO-ANTIBODY COMPLEX, COMPLEX (IMMUNOGLOBULIN-AUTOANTIGEN) complex; COMPLEX (IMMUNOGLOBULIN/AUTOANTIGEN)
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.97
Radius of gyration Rg (electron density) rg_electron33.04
Forward intensity I(0) i081323900.00
Molecular weight molecular_weight70646.0 kDa
Excluded volume excluded_volume88013 ų
Envelope volume envelope_volume118760 ų
Hydration-shell volume shell_volume32641 ų
Envelope diameter envelope_diameter126.9
Shell Rg shell_rg36.62
Envelope Rg envelope_rg33.58
Shape Rg shape_rg32.99
Total Rg total_rg33.50
Total atoms total_atoms4977
Residues n_residues644
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 dmax120.0
Rg (real space) rg_real33.43
Rg uncertainty (real space) rg_real_error1.32
I(0) (real space) i0_real8.1320e+07
I(0) uncertainty (real space) i0_real_error1.4980e+06
Rg (reciprocal space) rg_reciprocal33.24
I(0) (reciprocal space) i0_reciprocal81310000.0000
Solution quality estimate total_estimate0.8127
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.0
Skewness Skewness skewness0.652
Kurtosis Kurtosis kurtosis0.047
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7775000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.649; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.691; Smooth: 0.924

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1adqa1
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)
Domain ID domain_idd1adqa2
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)
Domain ID domain_idd1adqh1
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_idd1adqh2
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)
Domain ID domain_idd1adql1
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_idd1adql2
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)

CATH v4.4 (6 domains)

Domain ID domain_id1adqA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1adqA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1adqH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1adqH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1adqL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1adqL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (2)

9. Files and Curves (10)