4MHL | pdb_00004mhl

The crystal structure of human interleukin-11

• PDB DOI: https://doi.org/10.2210/pdb4MHL/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-29 Released: 2014-09-03 
• Deposition Author(s): Griffin, M.D.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.242 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.184 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

The structure of human interleukin-11 reveals receptor-binding site features and structural differences from interleukin-6.

Putoczki, T.L., Dobson, R.C., Griffin, M.D.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2277-2285

• PubMed: 25195742 
• DOI: https://doi.org/10.1107/S1399004714012267
• Primary Citation Related Structures: 
  4MHL


• PubMed Abstract: 
  

  Interleukin (IL)-11 is a multifunctional member of the IL-6 family of cytokines. Recombinant human IL-11 is administered as a standard clinical treatment for chemotherapy-induced thrombocytopaenia. Recently, a new role for IL-11 signalling as a potent driver of gastrointestinal cancers has been identified, and it has been demonstrated to be a novel therapeutic target for these diseases. Here, the crystal structure of human IL-11 is reported and the structural resolution of residues previously identified as important for IL-11 activity is presented. While IL-11 is thought to signal via a complex analogous to that of IL-6, comparisons show important differences between the two cytokines and it is suggested that IL-11 engages GP130 differently to IL-6. In addition to providing a structural platform for further study of IL-11, these data offer insight into the binding interactions of IL-11 with each of its receptors and the structural mechanisms underlying agonist and antagonist variants of the protein.

---

Organizational Affiliation: 
• Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.
Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8020, New Zealand.
Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 19.39 kDa 
• Atom Count: 1,309 
• Modeled Residue Count: 161 
• Deposited Residue Count: 177 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-11	A	177	Homo sapiens	Mutation(s): 0  Gene Names: IL11
UniProt & NIH Common Fund Data Resources
Find proteins for P20809 (Homo sapiens) Explore P20809  Go to UniProtKB:  P20809
PHAROS:  P20809 GTEx:  ENSG00000095752

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ARF	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	FORMAMIDE C H3 N O ZHNUHDYFZUAESO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.242 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.184 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.862	α = 90
b = 28.169	β = 90
c = 41.806	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-03 
Deposition Author(s): Griffin, M.D.W.

Revision History  

• Version 1.0: 2014-09-03
  Type: Initial release
  
• Version 1.1: 2014-10-22
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description