6BG7

Crystal structure of G107A mutant of human macrophage migration inhibitory factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Nanosecond Dynamics Regulate the MIF-Induced Activity of CD74.

Pantouris, G.Ho, J.Shah, D.Syed, M.A.Leng, L.Bhandari, V.Bucala, R.Batista, V.S.Loria, J.P.Lolis, E.J.

(2018) Angew. Chem. Int. Ed. Engl. 57: 7116-7119

  • DOI: 10.1002/anie.201803191
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Macrophage migration inhibitory factor (MIF) activates CD74, which leads to severe disorders including inflammation, autoimmune diseases and cancer under pathological conditions. Molecular dynamics (MD) simulations up to one microsecond revealed dyna ...

    Macrophage migration inhibitory factor (MIF) activates CD74, which leads to severe disorders including inflammation, autoimmune diseases and cancer under pathological conditions. Molecular dynamics (MD) simulations up to one microsecond revealed dynamical correlation between a residue located at the opening of one end of the MIF solvent channel, previously thought to be a consequence of homotrimerization, and residues in a distal region responsible for CD74 activation. Experiments verified the allosteric regulatory site and identified a pathway to this site via the MIF β-strands. The reported findings provide fundamental insights on a dynamic mechanism that controls the MIF-induced activation of CD74.


    Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,School of Chemistry, University of New South Wales, Sydney, NSW, 2052, Australia.,Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06510, USA.,Department of Pharmacology, School of Medicine, Yale University, New Haven, CT, 06510, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Section of Neonatal-Perinatal Medicine, Department of Pediatrics, Drexel University College of Medicine, Philadelphia, PA, USA.,Department of Pediatrics, Yale School of Medicine, New Haven, CT, 06510, USA.,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06510, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage migration inhibitory factor
A, B, C
114Homo sapiensMutation(s): 1 
Gene Names: MIF (GLIF, MMIF)
EC: 5.3.2.1
Find proteins for P14174 (Homo sapiens)
Go to Gene View: MIF
Go to UniProtKB:  P14174
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, B
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.198 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 95.863α = 90.00
b = 95.863β = 90.00
c = 103.712γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Data collection, Database references