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- EMDB-21460: Cryo-EM structure of SLC40/ferroportin in complex with Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-21460
TitleCryo-EM structure of SLC40/ferroportin in complex with Fab
Map datastructure of SLC40/ferroportin in complex with Fab
Sample
  • Complex: Cryo-EM map of SLC40/ferroportin in complex with Fab
    • Protein or peptide: Solute carrier family 40 protein
    • Protein or peptide: 11F9 light-chain
    • Protein or peptide: 11F9 heavy-chain
  • Ligand: COBALT (II) ION
  • Ligand: water
KeywordsSLC40 / Fpn / ferroportin / iron / transporter / cobalt / 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: 3.0 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
DepositionFeb 26, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vyh
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21460.png

Downloads & links

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Map

FileDownload / File: emd_21460.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of SLC40/ferroportin in complex with Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 200 pix.
= 222.8 Å		1.11 Å/pix.
x 200 pix.
= 222.8 Å		1.11 Å/pix.
x 200 pix.
= 222.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.114 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.03
Minimum - Maximum-0.1780855 - 0.2829512
Average (Standard dev.)-0.000008440332 (±0.0061561475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 222.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1141.1141.114
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z222.800222.800222.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1780.283-0.000

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Supplemental data

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Sample components

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Entire : Cryo-EM map of SLC40/ferroportin in complex with Fab

EntireName: Cryo-EM map of SLC40/ferroportin in complex with Fab
Components
  • Complex: Cryo-EM map of SLC40/ferroportin in complex with Fab
    • Protein or peptide: Solute carrier family 40 protein
    • Protein or peptide: 11F9 light-chain
    • Protein or peptide: 11F9 heavy-chain
  • Ligand: COBALT (II) ION
  • Ligand: water

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Supramolecule #1: Cryo-EM map of SLC40/ferroportin in complex with Fab

SupramoleculeName: Cryo-EM map of SLC40/ferroportin in complex with Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Carlito syrichta (Philippine tarsier)

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Macromolecule #1: Solute carrier family 40 protein

MacromoleculeName: Solute carrier family 40 protein / type: protein_or_peptide / ID: 1 / 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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Macromolecule #2: 11F9 light-chain

MacromoleculeName: 11F9 light-chain / type: protein_or_peptide / ID: 2 / 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 #3: 11F9 heavy-chain

MacromoleculeName: 11F9 heavy-chain / type: protein_or_peptide / ID: 3 / 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 #4: COBALT (II) ION

MacromoleculeName: COBALT (II) ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CO
Molecular weightTheoretical: 58.933 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
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 recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215752
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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