Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.25 kDa 
• Atom Count: 2549 
• Modelled Residue Count: 290 
• Deposited Residue Count: 290 
• Unique protein chains: 1

3L5I

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

• PDB DOI: 10.2210/pdb3L5I/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-22 Released: 2010-05-12 
• Deposition Author(s): Kershaw, N.J., Zhang, J.-G., Garrett, T.P.J., Czabotar, P.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.222 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Literature

Crystal structure of the entire ectodomain of gp130: insights into the molecular assembly of the tall cytokine receptor complexes.

Xu, Y., Kershaw, N.J., Luo, C.S., Soo, P., Pocock, M.J., Czabotar, P.E., Hilton, D.J., Nicola, N.A., Garrett, T.P., Zhang, J.G.

(2010) J Biol Chem 285: 21214-21218

• PubMed: 20489211 
• DOI: 10.1074/jbc.C110.129502
• Primary Citation of Related Structures:  
  3L5H, 3L5I, 3L5J


• PubMed Abstract: 
  

gp130 is the shared signal-transducing receptor subunit for the large and important family of interleukin 6-like cytokines. Previous x-ray structures of ligand-receptor complexes of this family lack the three membrane-proximal domains that are essential for signal transduction. Here we report the crystal structure of the entire extracellular portion of human gp130 (domains 1-6, D1-D6) at 3.6 A resolution, in an unliganded form, as well as a higher resolution structure of the membrane-proximal fibronectin type III domains (D4-D6) at 1.9 A. This represents the first atomic resolution structure of the complete ectodomain of any "tall" cytokine receptor. These structures show that other than a reorientation of the D1 domain, there is little structural change in gp130 upon ligand binding. They also reveal that the interface between the D4 and D5 domains forms an acute bend in the gp130 structure. Key residues at this interface are highly conserved across the entire tall receptor family, suggesting that this acute bend may be a common feature of these receptors. Importantly, this geometry positions the C termini of the membrane-proximal fibronectin type III domains of the tall cytokine receptors in close proximity within the transmembrane complex, favorable for receptor-associated Janus kinases to trans-phosphorylate and activate each other.

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Organizational Affiliation: 

Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-6 receptor subunit beta	A	290	Homo sapiens	Mutation(s): 0  Gene Names: GP130, IL6ST
UniProt & NIH Common Fund Data Resources
Find proteins for P40189 (Homo sapiens) Explore P40189  Go to UniProtKB:  P40189
PHAROS:  P40189 GTEx:  ENSG00000134352

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], P [auth A], R [auth A], S [auth A], U [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	O [auth A], Q [auth A], T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.222 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.565	α = 90
b = 75.347	β = 90
c = 107.185	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-22 
• Released Date: 2010-05-12 
Deposition Author(s): Kershaw, N.J., Zhang, J.-G., Garrett, T.P.J., Czabotar, P.E.

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-04-05
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Refinement description