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Yorodumi- EMDB-27497: Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27497 | |||||||||||||||
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Title | Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc | |||||||||||||||
Map data | Cryo-EM map of human ferroportin/slc40 bound to Ca2 | |||||||||||||||
Sample |
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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) / mouse (mice) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||
Authors | Shen J / Wilbon AS / Pan Y / Zhou M | |||||||||||||||
Funding support | United States, 4 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27497.map.gz | 15 MB | EMDB map data format | |
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Header (meta data) | emd-27497-v30.xml emd-27497.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_27497.png | 55.6 KB | ||
Others | emd_27497_half_map_1.map.gz emd_27497_half_map_2.map.gz | 28.2 MB 28.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27497 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27497 | HTTPS FTP |
-Validation report
Summary document | emd_27497_validation.pdf.gz | 546.9 KB | Display | EMDB validaton report |
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Full document | emd_27497_full_validation.pdf.gz | 546.4 KB | Display | |
Data in XML | emd_27497_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_27497_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27497 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27497 | HTTPS FTP |
-Related structure data
Related structure data | 8dl6MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27497.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of human ferroportin/slc40 bound to Ca2 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half A map of human ferroportin/slc40 bound to Ca2
File | emd_27497_half_map_1.map | ||||||||||||
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Annotation | Half_A map of human ferroportin/slc40 bound to Ca2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half B map of human ferroportin/slc40 bound to Ca2
File | emd_27497_half_map_2.map | ||||||||||||
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Annotation | Half_B map of human ferroportin/slc40 bound to Ca2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc
Entire | Name: Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc |
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Components |
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-Supramolecule #1: Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc
Supramolecule | Name: Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Solute carrier family 40 member 1
Macromolecule | Name: Solute carrier family 40 member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 63.386621 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MTRAGDHNRQ RGCCGSLADY LTSAKFLLYL GHSLSTWGDR MWHFAVSVFL VELYGNSLLL TAVYGLVVAG SVLVLGAIIG DWVDKNARL KVAQTSLVVQ NVSVILCGII LMMVFLHKHE LLTMYHGWVL TSCYILIITI ANIANLASTA TAITIQRDWI V VVAGEDRS ...String: MTRAGDHNRQ RGCCGSLADY LTSAKFLLYL GHSLSTWGDR MWHFAVSVFL VELYGNSLLL TAVYGLVVAG SVLVLGAIIG DWVDKNARL KVAQTSLVVQ NVSVILCGII LMMVFLHKHE LLTMYHGWVL TSCYILIITI ANIANLASTA TAITIQRDWI V VVAGEDRS KLANMNATIR RIDQLTNILA PMAVGQIMTF GSPVIGCGFI SGWNLVSMCV EYVLLWKVYQ KTPALAVKAG LK EEETELK QLNLHKDTEP KPLEGTHLMG VKDSNIHELE HEQEPTCASQ MAEPFRTFRD GWVSYYNQPV FLAGMGLAFL YMT VLGFDC ITTGYAYTQG LSGSILSILM GASAITGIMG TVAFTWLRRK CGLVRTGLIS GLAQLSCLIL CVISVFMPGS PLDL SVSPF EDIRSRFIQG ESITPTKIPE ITTEIYMSNG SNSANIVPET SPESVPIISV SLLFAGVIAA RIGLWSFDLT VTQLL QENV IESERGIING VQNSMNYLLD LLHFIMVILA PNPEAFGLLV LISVSFVAMG HIMYFRFAQN TLGNKLFACG PDAKEV RKE NQANTSVVEN LYFQ |
-Macromolecule #2: 11F9 light-chain
Macromolecule | Name: 11F9 light-chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: mouse (mice) |
Molecular weight | Theoretical: 23.493885 KDa |
Sequence | String: DIVMTQSQKF MSTSVGDRVS ITCKASQNVG TAVAWYQKKP GQSPKLLIYS ASNRYSGVPD RFTGSGSGTD FTLTISNMQS EDLADYFCQ QYGSYPLTFG SGTKLEIKEA EAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String: DIVMTQSQKF MSTSVGDRVS ITCKASQNVG TAVAWYQKKP GQSPKLLIYS ASNRYSGVPD RFTGSGSGTD FTLTISNMQS EDLADYFCQ QYGSYPLTFG SGTKLEIKEA EAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNE |
-Macromolecule #3: 11F9 heavy-chain
Macromolecule | Name: 11F9 heavy-chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: mouse (mice) |
Molecular weight | Theoretical: 25.815039 KDa |
Sequence | String: MKCSWVIFFL MAVVTGVNSE VQLQQSGAEL VRPGALVKLS CKASGFNIKD YYMHWVKERP EQGLEWIGWI DPENGNTIYD PKFQGKASI TADTSSNTAY LQLSSLTSED TAVYYCARKR GYYGPYFDYW GQGTTLTVSS KTTAPSVYPL APVCGDTTGS S VTLGCLVK ...String: MKCSWVIFFL MAVVTGVNSE VQLQQSGAEL VRPGALVKLS CKASGFNIKD YYMHWVKERP EQGLEWIGWI DPENGNTIYD PKFQGKASI TADTSSNTAY LQLSSLTSED TAVYYCARKR GYYGPYFDYW GQGTTLTVSS KTTAPSVYPL APVCGDTTGS S VTLGCLVK GYFPEPVTLT WNSGSLSSGV HTFPAVLQSG LYTLSSSVTV TSSTWPSQSI TCNVAHPASS TKVDKKIEPA |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 1 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 305 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 437959 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |