9YYA | pdb_00009yya

Macrophage Migration Inhibitory Factor 1 from Necator Americanus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.240 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9YYA

This is version 1.1 of the entry. See complete history

Literature

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

Orkwis, J.A.Manjula, R.Lolis, E.J.

(2026) iScience 29: 116513-116513

  • DOI: https://doi.org/10.1016/j.isci.2026.116513
  • Primary Citation Related Structures: 
    9YI5, 9YIU, 9YY9, 9YYA

  • PubMed Abstract: 

    Parasite-derived homologs of the cytokine macrophage migration inhibitory factor (MIF) function as virulent factors during parasitic infection. Recent evidence suggests MIF-like products from multicellular helminthic species can be targeted to ameliorate parasite burden. Here, we identify a broad contingent of hypothetical MIF-like proteins from genomic helminth repositories and perform structure analysis to validate conserved homology. Further, we employ a diverse subset of MIF-specific assays to establish cross-species functionality of helminth MIF proteins, including native enzymatic activity, binding to cognate receptor CD74, direct interactions with human MIF, and signaling through chemokine receptors CXCR2 and CXCR4. We demonstrate that MIF-like proteins retain a preserved architecture but are capable of diverse physiological outcomes due to small changes in key components of the conserved MIF structure. This work simultaneously provides a mechanistic understanding of helminth virulence upon infection, while broadly examining the potential to neutralize MIF-like proteins for protection against various pathological species.


  • Organizational Affiliation
    • Department of Pharmacology, Yale School of Medicine, Yale University, New Haven, CT, USA.

Macromolecule Content 

  • Total Structure Weight: 155.5 kDa 
  • Atom Count: 11,068 
  • Modeled Residue Count: 1,407 
  • Deposited Residue Count: 1,416 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Macrophage migration inhibitory factor
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
118Necator americanusMutation(s): 0 
Gene Names: Necator_chrV.g17532NECAME_06445RB195_012742
UniProt
Find proteins for W2TWH5 (Necator americanus)
Explore W2TWH5 
Go to UniProtKB:  W2TWH5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW2TWH5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.240 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.632α = 90
b = 126.213β = 90
c = 155.766γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2026-08-05
    Changes: Database references