8C02: SLC40/ferroportin

Structure of SLC40/ferroportin in complex with synthetic nanobody Sy3 in occluded conformation. Determined by electron microscopy at 4.09 Å resolution. Released 22 Mar 2023.

Method: Electron microscopy
Resolution: 4.09 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 4,242
Mol. weight: 79.88 kDa
Released: 22 Mar 2023

Explore 8C02 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8C02 contains 20 α-helices and 12 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	19-21	3
α-helix	24-53	30
α-helix	58-85	28
α-helix	88-115	28
α-helix	117-121	5
α-helix	128-151	24
α-helix	152-159	8
α-helix	160-163	4
α-helix	167-198	32
α-helix	201-229	29
α-helix	232-235	4
α-helix	289-304	16
α-helix	308-317	10
α-helix	332-335	4
α-helix	339-366	28
α-helix	369-392	24
α-helix	452-482	31
α-helix	489-513	25
α-helix	520-545	26

Chain B: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	1
β-strand	13-15	3	2
β-strand	19-26	8	1
β-strand	36-41	6	3
β-strand	48-53	6	3
β-strand	60	1	3
β-strand	70-75	6	1
β-strand	80-86	7	1
α-helix	90-92	3
β-strand	94-104	11	3
β-strand	109-113	5	3
β-strand	117-119	3	3
β-strand	120-148	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Solute carrier family 40 member 1	A	protein	580	Homo sapiens	Q9NP59 (AlphaFold model)
Sybody3	B	protein	146	synthetic construct

Sequence of entity 1 (A), FASTA

>8C02_1 Solute carrier family 40 member 1 (chains A)
MSTRAGDHNRQRGCCGSLADYLTSAKFLLYLGHSLSTWGDRMWHFAVSVFLVELYGNSLL
LTAVYGLVVAGSVLVLGAIIGDWVDKNARLKVAQTSLVVQNVSVILCGIILMMVFLHKHE
LLTMYHGWVLTSCYILIITIANIANLASTATAITIQRDWIVVVAGEDRSKLANMNATIRR
IDQLTNILAPMAVGQIMTFGSPVIGCGFISGWNLVSMCVEYVLLWKVYQKTPALAVKAGL
KEEETELKQLNLHKDTEPKPLEGTHLMGVKDSNIHELEHEQEPTCASQMAEPFRTFRDGW
VSYYNQPVFLAGMGLAFLYMTVLGFDCITTGYAYTQGLSGSILSILMGASAITGIMGTVA
FTWLRRKCGLVRTGLISGLAQLSCLILCVISVFMPGSPLDLSVSPFEDIRSRFIQGESIT
PTKIPEITTEIYMSNGSNSANIVPETSPESVPIISVSLLFAGVIAARIGLWSFDLTVTQL
LQENVIESERGIINGVQNSMNYLLDLLHFIMVILAPNPEAFGLLVLISVSFVAMGHIMYF
RFAQNTLGNKLFACGPDAKEVRKENQANTSVVALEVLFQG

Sequence of entity 2 (B), FASTA

>8C02_2 Sybody3 (chains B)
QVQLVESGGGLVQAGGSLRLSCAASGFPVAWNEMRWYRQAPGKEREWVAAIASIGVTTYY
ADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNVKDYGMAFWYYDYWGQGTQVTVS
AGRAGEQKLISEEDLNSAVDHHHHHH

Primary citation

Structures of ferroportin in complex with its specific inhibitor vamifeport. Lehmann, E.F., Liziczai, M., Drozdzyk, K. et al. Elife (2023) 12. DOI 10.7554/eLife.83053 · PubMed

Other PDB entries of the same protein (UniProt Q9NP59 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WBV 2.5 Å, Structure of human ferroportin bound to hepcidin and cobalt in lipid nanodisc
8DL7 2.7 Å, Cryo-EM structure of human ferroportin/slc40 bound to minihepcidin PR73 in nanodisc
8DL6 3.0 Å, Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc
8DL8 3.0 Å, Cryo-EM structure of human ferroportin/slc40 bound to Co2+ in nanodisc
6W4S 3.2 Å, Structure of apo human ferroportin in lipid nanodisc
8BZY 3.24 Å, Structure of SLC40/ferroportin in complex with vamifeport and synthetic nanobody Sy3 in…
8C03 3.89 Å, Structure of SLC40/ferroportin in complex with vamifeport and synthetic nanobody Sy12 in…

Browse structure collections

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