1PVH

Crystal structure of leukemia inhibitory factor in complex with gp130


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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 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 ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
Interleukin-6 receptor beta chain
A, C
201Homo sapiensMutation(s): 0 
Gene Names: IL6ST
Find proteins for P40189 (Homo sapiens)
Go to Gene View: IL6ST
Go to UniProtKB:  P40189
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Leukemia inhibitory factor
B, D
169Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, D
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LIFKd: 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 = 79.710α = 90.00
b = 86.700β = 90.00
c = 146.430γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
CNSrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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