8DL6 | pdb_00008dl6

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 8DL6

This is version 1.2 of the entry. See complete history. 

Literature

Mechanism of Ca 2+ transport by ferroportin.

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

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.82947
  • Primary Citation 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.

Macromolecule Content 

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

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Solute carrier family 40 member 1577Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NP59
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
11F9 light-chainB [auth C]213Mus musculusMutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
11F9 heavy-chainC [auth D]238Mus musculusMutation(s): 0 

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK122784
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL086392
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL157473
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesR1223

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-05-28
    Changes: Data collection