8DL6

Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc

• PDB DOI: https://doi.org/10.2210/pdb8DL6/pdb
• EM Map EMD-27497: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2022-07-07 Released: 2023-01-25 
• Deposition Author(s): Shen, J., Wilbon, A.S., Pan, Y., Zhou, M.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Cancer Prevention and Research Institute of Texas (CPRIT)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanism of Ca 2+ transport by ferroportin.

Shen, J., Wilbon, A.S., Zhou, M., Pan, Y.

(2023) Elife 12

• PubMed: 36648329 
• DOI: https://doi.org/10.7554/eLife.82947
• Primary Citation of Related Structures:  
  8DL6


• PubMed Abstract: 
  

  Ferroportin (Fpn) is a transporter that releases ferrous ion (Fe ²⁺ ) from cells and is important for homeostasis of iron in circulation. Export of one Fe ²⁺ by Fpn is coupled to import of two H ⁺ to maintain charge balance. Here, we show that human Fpn (HsFpn) binds to and mediates Ca ²⁺ transport. We determine the structure of Ca ²⁺ -bound HsFpn and identify a single Ca ²⁺ binding site distinct from the Fe ²⁺ binding sites. Further studies validate the Ca ²⁺ binding site and show that Ca ²⁺ transport is not coupled to transport of another ion. In addition, Ca ²⁺ transport is significantly inhibited in the presence of Fe ²⁺ but not vice versa. Function of Fpn as a Ca ²⁺ uniporter may allow regulation of iron homeostasis by Ca ²⁺ .

---

Organizational Affiliation: 

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 112.74 kDa 
• Atom Count: 6,171 
• Modelled Residue Count: 874 
• Deposited Residue Count: 1,028 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 40 member 1	A	577	Homo sapiens	Mutation(s): 0  Gene Names: SLC40A1, FPN1, IREG1, SLC11A3, MSTP079 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
11F9 light-chain	B [auth C]	213	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
11F9 heavy-chain	C [auth D]	238	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Shen, J., Wilbon, A.S., Pan, Y., Zhou, M.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK122784
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL086392
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL157473
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	R1223

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Structure summary