6WBV

Structure of human ferroportin bound to hepcidin and cobalt in lipid nanodisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of hepcidin-bound ferroportin reveals iron homeostatic mechanisms.

Billesbolle, C.B.Azumaya, C.M.Kretsch, R.C.Powers, A.S.Gonen, S.Schneider, S.Arvedson, T.Dror, R.O.Cheng, Y.Manglik, A.

(2020) Nature 586: 807-811

  • DOI: 10.1038/s41586-020-2668-z
  • Primary Citation of Related Structures:  
    6W4S, 6W4V, 6WBV

  • PubMed Abstract: 
  • The serum level of iron in humans is tightly controlled by the action of the hormone hepcidin on the iron efflux transporter ferroportin. Hepcidin regulates iron absorption and recycling by inducing the internalization and degradation of ferroportin

    The serum level of iron in humans is tightly controlled by the action of the hormone hepcidin on the iron efflux transporter ferroportin. Hepcidin regulates iron absorption and recycling by inducing the internalization and degradation of ferroportin 1 . Aberrant ferroportin activity can lead to diseases of iron overload, such as haemochromatosis, or iron limitation anaemias 2 . Here we determine cryogenic electron microscopy structures of ferroportin in lipid nanodiscs, both in the apo state and in complex with hepcidin and the iron mimetic cobalt. These structures and accompanying molecular dynamics simulations identify two metal-binding sites within the N and C domains of ferroportin. Hepcidin binds ferroportin in an outward-open conformation and completely occludes the iron efflux pathway to inhibit transport. The carboxy terminus of hepcidin directly contacts the divalent metal in the ferroportin C domain. Hepcidin binding to ferroportin is coupled to iron binding, with an 80-fold increase in hepcidin affinity in the presence of iron. These results suggest a model for hepcidin regulation of ferroportin, in which only ferroportin molecules loaded with iron are targeted for degradation. More broadly, our structural and functional insights may enable more targeted manipulation of the hepcidin-ferroportin axis in disorders of iron homeostasis.


    Organizational Affiliation

    Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA. aashish.manglik@ucsf.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hepcidin B25Homo sapiensMutation(s): 0 
Gene Names: HAMPHEPCLEAP1UNQ487/PRO1003
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Major Facilitator Superfamily (MFS) Transporters
Protein: 
Ferroportin (FPN) Fe2+ transporter (SLC40A1), apo protein in nanodisc
Find proteins for P81172 (Homo sapiens)
Explore P81172 
Go to UniProtKB:  P81172
NIH Common Fund Data Resources
PHAROS:  P81172
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Solute carrier family 40 member 1 A605Homo sapiensMutation(s): 0 
Gene Names: SLC40A1FPN1IREG1SLC11A3MSTP079
EC: 7
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Major Facilitator Superfamily (MFS) Transporters
Protein: 
Ferroportin (FPN) Fe2+ transporter (SLC40A1), apo protein in nanodisc
Find proteins for Q9NP59 (Homo sapiens)
Explore Q9NP59 
Go to UniProtKB:  Q9NP59
NIH Common Fund Data Resources
PHAROS:  Q9NP59
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab45D8 Light Chain L218Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fab45D8 Heavy Chain H220Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGA
Query on AGA

Download Ideal Coordinates CCD File 
A
(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
C19 H36 O10 P
UQSXQYRZHMGKIE-DLBZAZTESA-M
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States1DP5OD023048

Revision History 

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references