8UR4 | pdb_00008ur4

Crystal Structure of macrophage migration inhibitory factor (MIF) from Trichomonas vaginalis (I4122 form)

• PDB DOI: https://doi.org/10.2210/pdb8UR4/pdb

• Classification: CYTOKINE
• Organism(s): Trichomonas vaginalis G3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-25 Released: 2024-03-20 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.280 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.259 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: experimental

Literature

Structures of Trichomonas vaginalis macrophage migratory inhibitory factor.

Srivastava, A., Nair, A., Dawson, O.C.O., Gao, R., Liu, L., Craig, J.K., Battaile, K.P., Harmon, E.K., Barrett, L.K., Van Voorhis, W.C., Subramanian, S., Myler, P.J., Lovell, S., Asojo, O.A., Darwiche, R.

(2024) Acta Crystallogr F Struct Biol Commun 80: 341-347

• PubMed: 39601418 
• DOI: https://doi.org/10.1107/S2053230X24011105
• Primary Citation Related Structures: 
  8UR2, 8UR4, 8UZ4


• PubMed Abstract: 
  

  The unicellular parasitic protozoan Trichomonas vaginalis causes trichomoniasis, the most prevalent nonviral sexually transmitted disease globally. T. vaginalis evades host immune responses by producing homologs of host proteins, including cytokines such as macrophage migration inhibitory factor. T. vaginalis macrophage migration inhibitory factor (TvMIF) helps to facilitate the survival of T. vaginalis during nutritional stress conditions, increases prostate cell proliferation and invasiveness, and induces inflammation-related cellular pathways, thus mimicking the ability of human MIF to increase inflammation and cell proliferation. The production, crystallization and three structures of N-terminally hexahistidine-tagged TvMIF reveal a prototypical MIF trimer with a topology similar to that of human homologs (hMIF-1 and hMIF-2). The N-terminal tag obscures the expected pyruvate-binding site. The similarity of TvMIF to its human homologs can be exploited for structure-based drug discovery.

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Organizational Affiliation: 
• California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
Reedy High School, 3003 Stonebrook Parkway, Frisco, Texas, USA.
Grafton High School, 403 Grafton Drive, Yorktown, Virginia, USA.
Protein Structure and X-ray Crystallography Laboratory, 2034 Becker Drive, Lawrence, KS 66047, USA.
Center for Emerging and Re-emerging Infectious Diseases (CERID), Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA.
NYX, New York Structural Biology Center, Upton, New York, USA.
Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington, USA.
Dartmouth Cancer Center, One Medical Center Drive, Lebanon, NH 03756, USA.
Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.

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: 44.71 kDa 
• Atom Count: 2,581 
• Modeled Residue Count: 339 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MACROPHAGE MIGRATION INHIBITORY FACTOR	A, B, C	136	Trichomonas vaginalis G3	Mutation(s): 0  Gene Names: TVAG_219770 EC: 5.3.3.12 (UniProt), 5.3.2.1 (UniProt)
UniProt
Find proteins for A2DXT4 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2DXT4  Go to UniProtKB:  A2DXT4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], E [auth A], F [auth A], G [auth B], H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.280 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.259 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m38ur4

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.871	α = 90
b = 109.871	β = 90
c = 125.883	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-20 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2024-03-20
  Type: Initial release
  
• Version 1.1: 2024-12-11
  Changes: Database references, Structure summary