8C03

Structure of SLC40/ferroportin in complex with vamifeport and synthetic nanobody Sy12 in outward-facing conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structures of ferroportin in complex with its specific inhibitor vamifeport.

Lehmann, E.F.Liziczai, M.Drozdzyk, K.Altermatt, P.Langini, C.Manolova, V.Sundstrom, H.Durrenberger, F.Dutzler, R.Manatschal, C.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.83053
  • Primary Citation of Related Structures:  
    8BZY, 8C02, 8C03

  • PubMed Abstract: 

    A central regulatory mechanism of iron homeostasis in humans involves ferroportin (FPN), the sole cellular iron exporter, and the peptide hormone hepcidin, which inhibits Fe 2+ transport and induces internalization and degradation of FPN. Dysregulation of the FPN/hepcidin axis leads to diverse pathological conditions, and consequently, pharmacological compounds that inhibit FPN-mediated iron transport are of high clinical interest. Here, we describe the cryo-electron microscopy structures of human FPN in complex with synthetic nanobodies and vamifeport (VIT-2763), the first clinical-stage oral FPN inhibitor. Vamifeport competes with hepcidin for FPN binding and is currently in clinical development for β-thalassemia and sickle cell disease. The structures display two distinct conformations of FPN, representing outward-facing and occluded states of the transporter. The vamifeport site is located in the center of the protein, where the overlap with hepcidin interactions underlies the competitive relationship between the two molecules. The introduction of point mutations in the binding pocket of vamifeport reduces its affinity to FPN, emphasizing the relevance of the structural data. Together, our study reveals conformational rearrangements of FPN that are of potential relevance for transport, and it provides initial insight into the pharmacological targeting of this unique iron efflux transporter.


  • Organizational Affiliation

    Department of Biochemistry, University of Zurich, Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 40 member 1580Homo sapiensMutation(s): 0 
Gene Names: SLC40A1FPN1IREG1SLC11A3MSTP079
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP59 (Homo sapiens)
Explore Q9NP59 
Go to UniProtKB:  Q9NP59
PHAROS:  Q9NP59
GTEx:  ENSG00000138449 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NP59
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SZU (Subject of Investigation/LOI)
Query on SZU

Download Ideal Coordinates CCD File 
B [auth A]2-[2-[2-(1~{H}-benzimidazol-2-yl)ethylamino]ethyl]-~{N}-[(3-fluoranylpyridin-2-yl)methyl]-1,3-oxazole-4-carboxamide
C21 H21 F N6 O2
KNYVRFXIVWUGBZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 2.0: 2023-05-24
    Changes: Non-polymer description
  • Version 2.1: 2024-07-24
    Changes: Data collection