Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83690.83 
• Atom Count: 5834 
• Residue Count: 740 
• Unique protein chains: 2

1PVH

Crystal structure of leukemia inhibitory factor in complex with gp130

• DOI: 10.2210/pdb1PVH/pdb

• Classification: signaling protein/cytokine
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2003-06-27 Released: 2003-10-14 
• Deposition Author(s): Boulanger, M.J., Bankovich, A.J., Kortemme, T., Baker, D., Garcia, K.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.289 
• R-Value Work: 0.248 

Literature

Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130.

Boulanger, M.J., Bankovich, A.J., Kortemme, T., Baker, D., Garcia, K.C.

(2003) Mol.Cell 12: 577-589

• PubMed: 14527405 


• PubMed Abstract: 
  

Gp130 is a shared cell-surface signaling receptor for at least ten different hematopoietic cytokines, but the basis of its degenerate recognition properties is unknown. We have determined the crystal structure of human leukemia inhibitory factor (LIF) bound to the cytokine binding region (CHR) of gp130 at 2.5 A resolution. Strikingly, we find that the shared binding site on gp130 has an entirely rigid core, while the LIF binding interface diverges sharply in structure and chemistry from that of other gp130 ligands. Dissection of the LIF-gp130 interface, along with comparative studies of other gp130 cytokines, reveal that gp130 has evolved a "thermodynamic plasticity" that is relatively insensitive to ligand structure, to enable crossreactivity. These observations reveal a novel and alternative mechanism for degenerate recognition from that of structural plasticity.

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Organizational Affiliation: 

Department of Microbiology and Immunology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 94305, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Interleukin-6 receptor beta chain	A, C	201	Homo sapiens	Mutation(s): 0  Gene Names: IL6ST
Find proteins for P40189 (Homo sapiens) Go to Gene View: IL6ST Go to UniProtKB:  P40189

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Leukemia inhibitory factor	B, D	169	Homo sapiens	Mutation(s): 0  Gene Names: LIF (HILDA)
Find proteins for P15018 (Homo sapiens) Go to Gene View: LIF Go to UniProtKB:  P15018

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
IOD	A, D	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LIF	Kd: 80 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.289 
• R-Value Work: 0.248 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 79.710	α = 90.00
b = 86.700	β = 90.00
c = 146.430	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
HKL-2000	data reduction
CNS	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-27 
• Released Date: 2003-10-14 
• Deposition Author(s): Boulanger, M.J., Bankovich, A.J., Kortemme, T., Baker, D., Garcia, K.C.

Revision History 

• Version 1.0: 2003-10-14
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance