8DL6: Human ferroportin/slc40

Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc. Determined by electron microscopy at 3.0 Å resolution. Released 25 Jan 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 6,171
Mol. weight: 112.74 kDa
Ligands: CA
Released: 25 Jan 2023

Explore 8DL6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DL6 contains 33 α-helices and 40 β-strands across 3 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: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	16-22	7
α-helix	25-54	30
α-helix	59-84	26
α-helix	88-115	28
α-helix	117-123	7
α-helix	127-152	26
α-helix	153-159	7
α-helix	160-162	3
α-helix	167-196	30
α-helix	201-227	27
α-helix	231-233	3
α-helix	290-304	15
α-helix	308-316	9
α-helix	326-334	9
α-helix	341-367	27
α-helix	369-392	24
α-helix	453-483	31
α-helix	486-488	3
α-helix	491-513	23
α-helix	517-543	27

Chain C: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	24-25	2	1
β-strand	30-33	4	2
β-strand	38-45	8	1
β-strand	50	1	3
β-strand	53-58	6	2
β-strand	65-69	5	2
β-strand	73-74	2	2
α-helix	75	1
β-strand	82-87	6	1
β-strand	88	1	3
β-strand	90-96	7	1
β-strand	105-110	6	2
α-helix	116	1
β-strand	118	1	2
β-strand	122-126	5	2
α-helix	132-134	3
β-strand	137-138	2	4
α-helix	139-141	3
α-helix	142-146	5
β-strand	150-159	10	4
β-strand	165-170	6	5
β-strand	174	1	5
β-strand	179-183	5	4
β-strand	193-201	9	4
α-helix	203-207	5
β-strand	212-217	6	5
β-strand	225-228	4	5

Chain D: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	6
β-strand	29-31	3	7
β-strand	36-44	9	6
α-helix	48-50	3
β-strand	52-58	7	7
β-strand	64-71	8	7
β-strand	76-79	4	7
α-helix	81-86	6
β-strand	87-92	6	6
β-strand	97-103	7	6
α-helix	107-109	3
β-strand	111-118	8	7
β-strand	129	1	7
β-strand	133-137	5	7
β-strand	145-146	2	8
β-strand	163-170	8	8
β-strand	178	1	9
α-helix	180-182	3
β-strand	188-190	3	8
α-helix	191-193	3
β-strand	194-196	3	8
β-strand	199-206	8	8
α-helix	210-212	3
β-strand	219-222	4	9
β-strand	231-234	4	9
α-helix	235-237	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Solute carrier family 40 member 1	A	protein	577	Homo sapiens	Q9NP59 (AlphaFold model)
11F9 light-chain	C	protein	213	Mus musculus
11F9 heavy-chain	D	protein	238	Mus musculus

Sequence of entity 1 (A), FASTA

>8DL6_1 Solute carrier family 40 member 1 (chains A)
MTRAGDHNRQRGCCGSLADYLTSAKFLLYLGHSLSTWGDRMWHFAVSVFLVELYGNSLLL
TAVYGLVVAGSVLVLGAIIGDWVDKNARLKVAQTSLVVQNVSVILCGIILMMVFLHKHEL
LTMYHGWVLTSCYILIITIANIANLASTATAITIQRDWIVVVAGEDRSKLANMNATIRRI
DQLTNILAPMAVGQIMTFGSPVIGCGFISGWNLVSMCVEYVLLWKVYQKTPALAVKAGLK
EEETELKQLNLHKDTEPKPLEGTHLMGVKDSNIHELEHEQEPTCASQMAEPFRTFRDGWV
SYYNQPVFLAGMGLAFLYMTVLGFDCITTGYAYTQGLSGSILSILMGASAITGIMGTVAF
TWLRRKCGLVRTGLISGLAQLSCLILCVISVFMPGSPLDLSVSPFEDIRSRFIQGESITP
TKIPEITTEIYMSNGSNSANIVPETSPESVPIISVSLLFAGVIAARIGLWSFDLTVTQLL
QENVIESERGIINGVQNSMNYLLDLLHFIMVILAPNPEAFGLLVLISVSFVAMGHIMYFR
FAQNTLGNKLFACGPDAKEVRKENQANTSVVENLYFQ

Sequence of entity 2 (C), FASTA

>8DL6_2 11F9 light-chain (chains C)
DIVMTQSQKFMSTSVGDRVSITCKASQNVGTAVAWYQKKPGQSPKLLIYSASNRYSGVPD
RFTGSGSGTDFTLTISNMQSEDLADYFCQQYGSYPLTFGSGTKLEIKEAEAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Sequence of entity 3 (D), FASTA

>8DL6_3 11F9 heavy-chain (chains D)
MKCSWVIFFLMAVVTGVNSEVQLQQSGAELVRPGALVKLSCKASGFNIKDYYMHWVKERP
EQGLEWIGWIDPENGNTIYDPKFQGKASITADTSSNTAYLQLSSLTSEDTAVYYCARKRG
YYGPYFDYWGQGTTLTVSSKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWN
SGSLSSGVHTFPAVLQSGLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Mechanism of Ca 2+ transport by ferroportin. Shen, J., Wilbon, A.S., Zhou, M. et al. Elife (2023) 12. DOI 10.7554/eLife.82947 · 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
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…
8C02 4.09 Å, Structure of SLC40/ferroportin in complex with synthetic nanobody Sy3 in occluded…

Browse structure collections

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