8VJ2

Crystal Structure of Macrophage migration inhibitory factor-1 (MIF1) from Onchocerca volvulus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.236 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of N-terminally hexahistidine-tagged Onchocerca volvulus macrophage migration inhibitory factor-1.

Kimble, A.D.Dawson, O.C.O.Liu, L.Subramanian, S.Cooper, A.Battaile, K.Craig, J.Harmon, E.Myler, P.Lovell, S.Asojo, O.A.

(2024) Acta Crystallogr F Struct Biol Commun 80: 328-334

  • DOI: https://doi.org/10.1107/S2053230X24010550
  • Primary Citation of Related Structures:  
    8VJ2

  • PubMed Abstract: 

    Onchocerca volvulus causes blindness, onchocerciasis, skin infections and devastating neurological diseases such as nodding syndrome. New treatments are needed because the currently used drug, ivermectin, is contraindicated in pregnant women and those co-infected with Loa loa. The Seattle Structural Genomics Center for Infectious Disease (SSGCID) produced, crystallized and determined the apo structure of N-terminally hexahistidine-tagged O. volvulus macrophage migration inhibitory factor-1 (His-OvMIF-1). OvMIF-1 is a possible drug target. His-OvMIF-1 has a unique jellyfish-like structure with a prototypical macrophage migration inhibitory factor (MIF) trimer as the `head' and a unique C-terminal `tail'. Deleting the N-terminal tag reveals an OvMIF-1 structure with a larger cavity than that observed in human MIF that can be targeted for drug repurposing and discovery. Removal of the tag will be necessary to determine the actual biological oligomer of OvMIF-1 because size-exclusion chomatographic analysis of His-OvMIF-1 suggests a monomer, while PISA analysis suggests a hexamer stabilized by the unique C-terminal tails.


  • Organizational Affiliation

    Department of Clinical Laboratory Science, College of Nursing and Allied Health Sciences, Howard University, 801 North Capitol Street, 4th Floor, Washington, DC 20002, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage migration inhibitory factor-1
A, B, C
136Onchocerca volvulusMutation(s): 0 
Gene Names: mif1
EC: 5.3.3.12 (UniProt), 5.3.2.1 (UniProt)
UniProt
Find proteins for Q963F7 (Onchocerca volvulus)
Explore Q963F7 
Go to UniProtKB:  Q963F7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ963F7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.441α = 90
b = 91.127β = 90
c = 132.487γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93022C00036
National Institutes of Health/Office of the DirectorUnited StatesS10OD030394

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references, Structure summary
  • Version 1.2: 2024-12-18
    Changes: Database references