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Yorodumi- PDB-8dl6: Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dl6 | |||||||||||||||
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Title | Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / SLC40 / Fpn / ferroportin / iron transporter / calcium / Ca2+ / human / nanodisc | |||||||||||||||
Function / homology | Function and homology information spleen trabecula formation / iron ion export across plasma membrane / Defective SLC40A1 causes hemochromatosis 4 (HFE4) (duodenum) / Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) / Defective CP causes aceruloplasminemia (ACERULOP) / Metal ion SLC transporters / lymphocyte homeostasis / iron ion transmembrane transporter activity / iron ion transmembrane transport / ferrous iron transmembrane transporter activity ...spleen trabecula formation / iron ion export across plasma membrane / Defective SLC40A1 causes hemochromatosis 4 (HFE4) (duodenum) / Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) / Defective CP causes aceruloplasminemia (ACERULOP) / Metal ion SLC transporters / lymphocyte homeostasis / iron ion transmembrane transporter activity / iron ion transmembrane transport / ferrous iron transmembrane transporter activity / endothelium development / peptide hormone binding / establishment of localization in cell / Iron uptake and transport / multicellular organismal-level iron ion homeostasis / synaptic vesicle / basolateral plasma membrane / intracellular iron ion homeostasis / transcription by RNA polymerase II / negative regulation of apoptotic process / apoptotic process / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||||||||
Authors | Shen, J. / Wilbon, A.S. / Pan, Y. / Zhou, M. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Elife / Year: 2023 Title: Mechanism of Ca transport by ferroportin. Authors: Jiemin Shen / Azaan Saalim Wilbon / Ming Zhou / Yaping Pan / Abstract: Ferroportin (Fpn) is a transporter that releases ferrous ion (Fe) from cells and is important for homeostasis of iron in circulation. Export of one Fe by Fpn is coupled to import of two H to maintain ...Ferroportin (Fpn) is a transporter that releases ferrous ion (Fe) from cells and is important for homeostasis of iron in circulation. Export of one Fe 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 transport. We determine the structure of Ca-bound HsFpn and identify a single Ca binding site distinct from the Fe binding sites. Further studies validate the Ca binding site and show that Ca transport is not coupled to transport of another ion. In addition, Ca transport is significantly inhibited in the presence of Fe but not vice versa. Function of Fpn as a Ca uniporter may allow regulation of iron homeostasis by Ca. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dl6.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dl6.ent.gz | 129.6 KB | Display | PDB format |
PDBx/mmJSON format | 8dl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dl6_validation.pdf.gz | 885.4 KB | Display | wwPDB validaton report |
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Full document | 8dl6_full_validation.pdf.gz | 893.9 KB | Display | |
Data in XML | 8dl6_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 8dl6_validation.cif.gz | 48.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/8dl6 ftp://data.pdbj.org/pub/pdb/validation_reports/dl/8dl6 | HTTPS FTP |
-Related structure data
Related structure data | 27497MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 63386.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC40A1, FPN1, IREG1, SLC11A3, MSTP079 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NP59 |
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#2: Antibody | Mass: 23493.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Antibody | Mass: 25815.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 305 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 437959 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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