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- EMDB-21684: Cryo-EM structure of SLC40/ferroportin with Fab in the presence o... -

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Basic information

Entry
Database: EMDB / ID: EMD-21684
TitleCryo-EM structure of SLC40/ferroportin with Fab in the presence of hepcidin
Map data
Sample
  • Complex: Cryo-EM map of SLC40/ferroportin with Fab in the presence of hepcidin
    • Protein or peptide: 11F9 Fab light-chain
    • Protein or peptide: 11F9 Fab heavy-chain
    • Protein or peptide: Solute carrier family 40 protein
KeywordsSLC40 / Fpn / ferroportin / iron transporter / hepcidin / MEMBRANE PROTEIN
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / peptide hormone binding / basolateral plasma membrane / intracellular iron ion homeostasis / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Ferroportin-1 / Ferroportin1 (FPN1) / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 40 member
Similarity search - Component
Biological speciesCarlito syrichta (Philippine tarsier) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsShen J / Ren Z
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK122784 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086392 United States
Cancer Prevention and Research Institute of Texas (CPRIT)R1223 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis of ion transport and inhibition in ferroportin.
Authors: Yaping Pan / Zhenning Ren / Shuai Gao / Jiemin Shen / Lie Wang / Zhichun Xu / Ye Yu / Preetham Bachina / Hanzhi Zhang / Xiao Fan / Arthur Laganowsky / Nieng Yan / Ming Zhou /
Abstract: Ferroportin is an iron exporter essential for releasing cellular iron into circulation. Ferroportin is inhibited by a peptide hormone, hepcidin. In humans, mutations in ferroportin lead to ...Ferroportin is an iron exporter essential for releasing cellular iron into circulation. Ferroportin is inhibited by a peptide hormone, hepcidin. In humans, mutations in ferroportin lead to ferroportin diseases that are often associated with accumulation of iron in macrophages and symptoms of iron deficiency anemia. Here we present the structures of the ferroportin from the primate Philippine tarsier (TsFpn) in the presence and absence of hepcidin solved by cryo-electron microscopy. TsFpn is composed of two domains resembling a clamshell and the structure defines two metal ion binding sites, one in each domain. Both structures are in an outward-facing conformation, and hepcidin binds between the two domains and reaches one of the ion binding sites. Functional studies show that TsFpn is an electroneutral H/Fe antiporter so that transport of each Fe is coupled to transport of two H in the opposite direction. Perturbing either of the ion binding sites compromises the coupled transport of H and Fe. These results establish the structural basis of metal ion binding, transport and inhibition in ferroportin and provide a blueprint for targeting ferroportin in pharmacological intervention of ferroportin diseases.
History
DepositionApr 10, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wik
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21684.png

Downloads & links

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Map

FileDownload / File: emd_21684.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.024342507 - 0.047095165
Average (Standard dev.)0.000002207595 (±0.0016652509)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.00002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z214.000214.000214.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ172172172
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0240.0470.000

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Supplemental data

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Sample components

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Entire : Cryo-EM map of SLC40/ferroportin with Fab in the presence of hepcidin

EntireName: Cryo-EM map of SLC40/ferroportin with Fab in the presence of hepcidin
Components
  • Complex: Cryo-EM map of SLC40/ferroportin with Fab in the presence of hepcidin
    • Protein or peptide: 11F9 Fab light-chain
    • Protein or peptide: 11F9 Fab heavy-chain
    • Protein or peptide: Solute carrier family 40 protein

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Supramolecule #1: Cryo-EM map of SLC40/ferroportin with Fab in the presence of hepcidin

SupramoleculeName: Cryo-EM map of SLC40/ferroportin with Fab in the presence of hepcidin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Carlito syrichta (Philippine tarsier)

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Macromolecule #1: 11F9 Fab light-chain

MacromoleculeName: 11F9 Fab light-chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.493885 KDa
SequenceString: 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

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Macromolecule #2: 11F9 Fab heavy-chain

MacromoleculeName: 11F9 Fab heavy-chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.815039 KDa
SequenceString: 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

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Macromolecule #3: Solute carrier family 40 protein

MacromoleculeName: Solute carrier family 40 protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Carlito syrichta (Philippine tarsier)
Molecular weightTheoretical: 63.705004 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSRAREQERQ GGCCRSLANY LTSAKFLLYL GHSLSTWGDR MWHFAVSVFL VELYGNSLLL TAVYGLVVAG SVLVLGAIIG DWVDKNARL KVAQTSLVIQ NVSVILCGII LMMVFLHKDE LLTMYHGWVL TSCYILIITI ANIANLASTA TAITIQRDWI V VVAGEDRS ...String:
MSRAREQERQ GGCCRSLANY LTSAKFLLYL GHSLSTWGDR MWHFAVSVFL VELYGNSLLL TAVYGLVVAG SVLVLGAIIG DWVDKNARL KVAQTSLVIQ NVSVILCGII LMMVFLHKDE LLTMYHGWVL TSCYILIITI ANIANLASTA TAITIQRDWI V VVAGEDRS KLANMNATVR RIDQLTNILA PMAVGQIMTY GSPVIGCGFI SGWNLVSMCV EYFLLWKVYQ KTPALAVKAA LK VEETELK QLNLHKDTEP KPLEGTHLMG EKDPNIHELE HEQEPTCASQ MAEPFRTFRD GWVSYYNQPI FLAGMGLAFL YMT VLGFDC ITTGYAYTQG LSGSVLSILM GASAITGIMG TVAFTWLRRK CGLVRTGLIS GWAQISCLIL CVISVFMPGS PLDL SVSPF EDIRSRFIQE ELITPTKIPE TIITTEMHIS NGSDLHIAPE ASPQSVPIIS VSLLFAGVIA ARIGLWSFDL TVTQL LQEN VIESERGIIN GVQNSMNYLL DLLHFIMVIL APNPEAFGLL VLISVSFVVM GHIMYFRFAQ KTLGNQLFVC GPDAKE VTN ENQSNTSVVE NLYQ

UniProtKB: Solute carrier family 40 member

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration13 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 305 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: SUPER-RESOLUTION / #1 - Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 214136
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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