6FVE

Macrophage Migration Inhibitory Factor (MIF) with Covalently Bound FITC

• PDB DOI: https://doi.org/10.2210/pdb6FVE/pdb

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


• Deposited: 2018-03-02 Released: 2018-06-06 
• Deposition Author(s): Samygina, V.R., Bourenkov, G., Sokolov, A.V.
• Funding Organization(s): RFBR

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.189 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 

Literature

Structural Study of the Complex Formed by Ceruloplasmin and Macrophage Migration Inhibitory Factor.

Sokolov, A.V., Dadinova, L.A., Petoukhov, M.V., Bourenkov, G., Dubova, K.M., Amarantov, S.V., Volkov, V.V., Kostevich, V.A., Gorbunov, N.P., Grudinina, N.A., Vasilyev, V.B., Samygina, V.R.

(2018) Biochemistry (Mosc) 83: 701-707

• PubMed: 30195326 
• DOI: https://doi.org/10.1134/S000629791806007X
• Primary Citation of Related Structures:  
  6FVE, 6FVH


• PubMed Abstract: 
  

  Macrophage migration inhibitory factor (MIF) is a key proinflammatory cytokine. Inhibitors of tautomerase activity of MIF are perspective antiinflammatory compounds. Ceruloplasmin, the copper-containing ferroxidase of blood plasma, is a noncompetitive inhibitor of tautomerase activity of MIF in the reaction with p-hydroxyphenylpyruvate. Small-angle X-ray scattering established a model of the complex formed by MIF and ceruloplasmin. Crystallographic analysis of MIF with a modified active site supports the model. The stoichiometry of 3 CP/MIF trimer complex was established using gel filtration. Conformity of novel data concerning the interaction regions in the studied proteins with previous biochemical data is discussed.

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Organizational Affiliation: 

Institute of Experimental Medicine, St. Petersburg, 197376, Russia.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.34 kDa 
• Atom Count: 3,266 
• Modelled Residue Count: 342 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage migration inhibitory factor	A, B [auth C], C [auth B]	114	Homo sapiens	Mutation(s): 0  Gene Names: MIF, GLIF, MMIF EC: 5.3.2.1 (PDB Primary Data), 5.3.3.12 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14174 (Homo sapiens) Explore P14174  Go to UniProtKB:  P14174
PHAROS:  P14174 GTEx:  ENSG00000240972

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6B9	D [auth A], F [auth C], G [auth B]	2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-5-[(E)-(sulfanylmethylidene)amino]benzoic acid C21 H13 N O5 S KDFRZGWCOSXMPY-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.189 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.783	α = 90
b = 70.644	β = 90
c = 89.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-06-06 
Deposition Author(s): Samygina, V.R., Bourenkov, G., Sokolov, A.V.

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Funding Organization	Location	Grant Number
RFBR	Russian Federation	15-54-74006

Revision History  

• Version 1.0: 2018-06-06
  Type: Initial release
  
• Version 1.1: 2018-09-19
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description