9I0N: Human sortilin ectodomain

Cryo-EM structure of human sortilin ectodomain. Determined by electron microscopy at 3.1 Å resolution. Released 17 Dec 2025.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 1
Atoms: 4,938
Mol. weight: 84.01 kDa
Ligands: NAG
Released: 17 Dec 2025

Explore 9I0N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I0N contains 9 α-helices and 64 β-strands across 1 chain. 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: 9 helices, 64 β-strands

Element	Residues	Length	Sheet
α-helix	59-64	6
β-strand	67-71	5	1
β-strand	80-84	5	2
β-strand	90-97	8	2
β-strand	108-114	7	2
β-strand	122-123	2	2
β-strand	133	1	3
α-helix	141-142	2
β-strand	149-152	4	4
β-strand	153	1	3
β-strand	164-167	4	4
β-strand	175-177	3	4
β-strand	183	1	5
β-strand	188-189	2	6
β-strand	197-200	4	6
β-strand	201	1	5
β-strand	206-209	4	6
β-strand	217-220	4	6
β-strand	223-228	6	7
β-strand	234-238	5	7
β-strand	251-256	6	7
β-strand	264-276	13	7
β-strand	279-285	7	7
β-strand	292-297	6	7
β-strand	305-306	2	7
β-strand	308	1	8
β-strand	312	1	7
β-strand	318-323	6	9
β-strand	328-333	6	9
α-helix	334	1
β-strand	340-346	7	9
β-strand	352	1	8
β-strand	353-361	9	9
β-strand	362	1	10
β-strand	369	1	10
β-strand	372-373	2	9
β-strand	381-386	6	9
β-strand	392-397	6	9
β-strand	405	1	9
α-helix	406-410	5
β-strand	421	1	11
β-strand	424	1	11
β-strand	426-429	4	12
α-helix	432-436	5
β-strand	446	1	12
β-strand	455-462	8	12
β-strand	471-475	5	12
β-strand	483-486	4	12
β-strand	490-495	6	13
β-strand	500-505	6	13
β-strand	511	1	14
β-strand	514-517	4	13
β-strand	525-527	3	13
β-strand	534	1	14
β-strand	535-540	6	1
β-strand	549-556	8	1
β-strand	563-570	8	1
β-strand	578	1	15
α-helix	579	1
α-helix	581-583	3
β-strand	584-588	5	16
β-strand	602	1	16
β-strand	605-612	8	16
β-strand	619	1	15
β-strand	628-632	5	16
β-strand	635	1	17
α-helix	637-639	3
β-strand	640-642	3	18
β-strand	646-647	2	19
β-strand	656-657	2	19
β-strand	682-684	3	18
α-helix	685	1
β-strand	693	1	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sortilin	A	protein	742	Homo sapiens	Q99523 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9I0N_1 Sortilin (chains A)
QDRLDAPPPPAAPLPRWSGPIGVSWGLRAAAAGGAFPRGGRWRRSAPGEDEECGRVRDFV
AKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVPLVIMTFGQSKLYRSEDYGKN
FKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRIFRSSDFAKNFVQTDLP
FHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVCLAKWGSDNTIFFTTYA
NGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASVMADKDTTRRIHVSTDQ
GDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIFTSDDRGIVYSKSLDRH
LYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRWTHLRKPENSECDATAK
NKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDAISVMVPDVYISDDGGY
SWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCWQTYTFTRDPIYFTGLA
SEPGARSMNISIWGFTESFLTSQWVSYTIDFKDILERNCEEKDYTIWLAHSTDPEDYEDG
CILGYKEQFLRLRKSSVCQNGRDYVVTKQPSICLCSLEDFLCDFGYYRPENDSKCVEQPE
LKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLKKKCTSNFLSPEKQNSK
SNSENLYFQSAGHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Molecular recognition of thyroglobulin by sortilin. Boniardi, I., Tanzi, G., Di Ianni, A. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-68658-z · PubMed

Other PDB entries of the same protein (UniProt Q99523 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3F6K 2.0 Å, Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with neurotensin
5MRI 2.0 Å, Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone…
3G2V 2.1 Å, VHS Domain of human GGA1 complexed with Sotilin C-terminal Phosphopeptide
3G2U 2.3 Å, VHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide
5MRH 2.5 Å, Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone 1
4PO7 2.66 Å, Structure of the Sortilin:neurotensin complex at excess neurotensin concentration
4MSL 2.7 Å, Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF40431
4N7E 2.7 Å, Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF38469
6X3L 2.7 Å, Sortilin-Progranulin Interaction With Compound 2
9R18 2.8 Å, Structure of Sortilin ECD in complex with TNFa-targeting SORTAC
8T8R 2.87 Å, Sortilin-PGRN peptide complex
6X48 2.9 Å, Sortilin-Progranulin Interaction With Compound 17

Browse structure collections

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