3l5j

Crystal structure of FnIII domains of human GP130 (Domains 4-6)

Method: X-RAY DIFFRACTION Dmax: 98.9 Å Quality: GOOD

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

Interleukin-6 receptor subunit beta

Homo sapiens

UniProt P40189

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 323–610 Fragment:UNP residues 323-610 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;PEG 8000, NaCl, Tris-HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K Resolution 3.04 Å R-free 0.265
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 323–610 Fragment:UNP residues 323-610 CL CHLORIDE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;PEG 8000, NaCl, Tris-HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K Resolution 3.04 Å R-free 0.265

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.

19 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL6RB_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–288; UniProt 323–610 Author chain B; PDBConstruct 1–288; UniProt 323–610

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 3l5j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3l5j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3l5j
Deposition date deposition_date2009-12-22
Structure title titleCrystal structure of FnIII domains of human GP130 (Domains 4-6)
Keywords keywordsCytokine Receptor, Fibronectin Type III domain, 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_guinier34.12
Radius of gyration Rg (electron density) rg_electron33.20
Forward intensity I(0) i058824200.00
Molecular weight molecular_weight60883.0 kDa
Excluded volume excluded_volume76114 ų
Envelope volume envelope_volume108630 ų
Hydration-shell volume shell_volume28172 ų
Envelope diameter envelope_diameter96.6
Shell Rg shell_rg38.86
Envelope Rg envelope_rg31.99
Shape Rg shape_rg33.20
Total Rg total_rg33.70
Total atoms total_atoms4300
Residues n_residues569
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 dmax98.9
Rg (real space) rg_real33.96
Rg uncertainty (real space) rg_real_error0.60
I(0) (real space) i0_real5.8820e+07
I(0) uncertainty (real space) i0_real_error7.2460e+05
Rg (reciprocal space) rg_reciprocal34.07
I(0) (reciprocal space) i0_reciprocal58830000.0000
Solution quality estimate total_estimate0.8970
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.9
Skewness Skewness skewness-0.110
Kurtosis Kurtosis kurtosis-0.892
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3056000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.900

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id3l5jA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3l5jA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3l5jA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3l5jB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3l5jB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3l5jB03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)