9YI5 | pdb_00009yi5

Macrophage Migration Inhibitory Factor 2 from Heligmosomoides polygyrus

• PDB DOI: https://doi.org/10.2210/pdb9YI5/pdb

• Classification: CYTOKINE
• Organism(s): Heligmosomoides polygyrus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-10-01 Released: 2025-11-05 
• Deposition Author(s): Orkwis, J.A., Lolis, E.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.176 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.150 (DCC) 

Starting Model: experimental

Literature

Helminth proteins recapitulate key structural motifs of MIF to facilitate immunomodulation of host receptors

Orkwis, J.A., Lolis, E.J.

To be published.

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: 12.18 kDa 
• Atom Count: 933 
• Modeled Residue Count: 114 
• Deposited Residue Count: 114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hpMIF2	A	114	Heligmosomoides polygyrus	Mutation(s): 0  Gene Names: FMJQ01000000

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.176 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.150 (DCC) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.631	α = 90
b = 67.631	β = 90
c = 46.946	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Orkwis, J.A., Lolis, E.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release