6W4S: Apo human ferroportin in lipid nanodisc

Structure of apo human ferroportin in lipid nanodisc. Determined by electron microscopy at 3.2 Å resolution. Released 9 Sept 2020.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 4,986
Mol. weight: 114.21 kDa
Released: 9 Sept 2020

Explore 6W4S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W4S contains 20 α-helices and 25 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 F: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	19-22	4
α-helix	26-54	29
α-helix	58-85	28
α-helix	88-115	28
α-helix	117-122	6
α-helix	126-153	28
α-helix	154-158	5
α-helix	159-161	3
α-helix	167-197	31
α-helix	201-229	29
α-helix	231-233	3
α-helix	293-303	11
α-helix	308-316	9
α-helix	328-334	7
α-helix	339-366	28
α-helix	371-392	22
α-helix	453-483	31
α-helix	489-513	25
α-helix	517-545	29

Chain H: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	17-25	9	1
β-strand	33-39	7	3
β-strand	45-51	7	3
β-strand	57-59	3	3
β-strand	66-72	7	1
β-strand	77-83	7	1
β-strand	91-98	8	3
β-strand	105-108	4	3
β-strand	112-114	3	3
β-strand	115-116	2	2

Chain L: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	4
β-strand	12-13	2	5
β-strand	19-24	6	4
β-strand	30-31	2	6
β-strand	34-35	2	6
β-strand	37-42	6	7
β-strand	49-52	4	7
β-strand	66-71	6	4
β-strand	74-79	6	4
β-strand	89-94	6	7
α-helix	100	1
β-strand	101-102	2	7
β-strand	106-107	2	7
β-strand	109-110	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Solute carrier family 40 member 1	F	protein	605	Homo sapiens	Q9NP59 (AlphaFold model)
Fab45D8 Heavy Chain	H	protein	220	Mus musculus
Fab45D8 Light Chain	L	protein	218	Mus musculus

Sequence of entity 1 (F), FASTA

>6W4S_1 Solute carrier family 40 member 1 (chains F)
MTRAGDHNRQRGCCGSLADYLTSAKFLLYLGHSLSTWGDRMWHFAVSVFLVELYGNSLLL
TAVYGLVVAGSVLVLGAIIGDWVDKNARLKVAQTSLVVQNVSVILCGIILMMVFLHKHEL
LTMYHGWVLTSCYILIITIANIANLASTATAITIQRDWIVVVAGEDRSKLANMNATIRRI
DQLTNILAPMAVGQIMTFGSPVIGCGFISGWNLVSMCVEYVLLWKVYQKTPALAVKAGLK
EEETELKQLNLHKDTEPKPLEGTHLMGVKDSNIHELEHEQEPTCASQMAEPFRTFRDGWV
SYYNQPVFLAGMGLAFLYMTVLGFDCITTGYAYTQGLSGSILSILMGASAITGIMGTVAF
TWLRRKCGLVRTGLISGLAQLSCLILCVISVFMPGSPLDLSVSPFEDIRSRFIQGESITP
TKIPEITTEIYMSNGSNSANIVPETSPESVPIISVSLLFAGVIAARIGLWSFDLTVTQLL
QENVIESERGIINGVQNSMNYLLDLLHFIMVILAPNPEAFGLLVLISVSFVAMGHIMYFR
FAQNTLGNKLFACGPDAKEVRKENQANTSVVGSGLEVLFQGPGAAEDQVDPRLIDGKHHH
HHHHH

Sequence of entity 2 (H), FASTA

>6W4S_2 Fab45D8 Heavy Chain (chains H)
EVQLQESGPGLAKPSQTLSLTCSVTGSSITSDYWNWIRKFPGNKLEYMGYISYSGSTYYN
PSLKSQISITRDTSKNHYYLQLNSVTTEDTATYYCARQGLRNWYFDVWGTGTTVTVSSAK
TTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLY
TLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEPRVP

Sequence of entity 3 (L), FASTA

>6W4S_3 Fab45D8 Light Chain (chains L)
DIVLTQSPASLPVSLGQRATISCRASKSVSASAYSYMHWYQQKPGQPPKPLIYLASNLES
GVPARFSGSGSGTDFTLNIHPVEEEDAATYYCQHNRELPYTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Structure of hepcidin-bound ferroportin reveals iron homeostatic mechanisms. Billesbolle, C.B., Azumaya, C.M., Kretsch, R.C. et al. Nature (2020) 586:807-811. DOI 10.1038/s41586-020-2668-z · 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
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…

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