4PO7: Sortilin

Structure of the Sortilin:neurotensin complex at excess neurotensin concentration. Determined by X-ray diffraction at 2.66 Å resolution. Released 23 Jul 2014.

Method: X-ray diffraction
Resolution: 2.66 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,518
Mol. weight: 81.72 kDa
Ligands: NAG
Released: 23 Jul 2014

Explore 4PO7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PO7 contains 19 α-helices and 67 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, 65 β-strands

Element	Residues	Length	Sheet
α-helix	59-64	6
β-strand	67-72	6	1
β-strand	78-83	6	2
β-strand	91-96	6	2
β-strand	97	1	3
β-strand	108	1	3
β-strand	111-114	4	2
β-strand	122-123	2	2
α-helix	125-128	4
β-strand	133	1	4
β-strand	139-141	3	5
α-helix	142	1
β-strand	149-152	4	5
β-strand	153	1	4
α-helix	154	1
β-strand	163-167	5	5
β-strand	175-178	4	5
β-strand	183	1	6
β-strand	188-190	3	7
β-strand	193-200	8	7
β-strand	201	1	6
β-strand	206-209	4	7
β-strand	217-220	4	7
β-strand	223-228	6	8
α-helix	230-232	3
β-strand	234-238	5	8
β-strand	251	1	9
β-strand	252-256	5	8
β-strand	264-265	2	8
β-strand	270-276	7	9
β-strand	279-285	7	9
β-strand	292-297	6	9
β-strand	305-306	2	9
β-strand	312	1	9
β-strand	318-323	6	10
β-strand	328-333	6	10
α-helix	334	1
β-strand	340-346	7	10
β-strand	353-361	9	10
β-strand	362	1	11
β-strand	369	1	11
β-strand	372-373	2	10
β-strand	381-386	6	10
β-strand	392-397	6	10
β-strand	404-406	3	10
β-strand	407	1	12
α-helix	408-410	3
α-helix	413-415	3
β-strand	426-429	4	12
α-helix	432-436	5
β-strand	446	1	12
β-strand	455-462	8	12
α-helix	469-470	2
β-strand	471-475	5	12
β-strand	483-486	4	12
β-strand	490-495	6	13
α-helix	496-498	3
β-strand	500-505	6	13
β-strand	511	1	1
β-strand	513-517	5	13
β-strand	525-528	4	13
β-strand	534-540	7	1
β-strand	549-556	8	1
β-strand	564-570	7	1
α-helix	571-573	3
β-strand	578	1	14
α-helix	581-583	3
β-strand	584-588	5	15
β-strand	602	1	15
β-strand	605-612	8	15
α-helix	613	1
β-strand	619	1	14
β-strand	628-632	5	15
α-helix	633-634	2
β-strand	635	1	16
α-helix	637-639	3
β-strand	640-642	3	17
β-strand	646-647	2	18
β-strand	656-657	2	18
α-helix	664-671	8
α-helix	674-677	4
β-strand	682-684	3	17
β-strand	693	1	16
α-helix	704-708	5

Chain N: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	2
β-strand	11-12	2	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sortilin	A	protein	685	Homo sapiens	Q99523 (AlphaFold model)
Neurotensin/neuromedin N	N, P	protein	13	Homo sapiens	P30990 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4PO7_1 Sortilin (chains A)
SAPGEDEECGRVRDFVAKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVPLVIM
TFGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRI
FRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVC
LAKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASV
MADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIF
TSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRW
THLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDA
ISVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCW
QTYTFTRDPIYFTGLASEPGARSMNISIWGFTESFLTSQWVSYTIDFKDILERNCEEKDY
TIWLAHSTDPEDYEDGCILGYKEQFLRLRKSSMCQNGRDYVVTKQPSICLCSLEDFLCDF
GYYRPENDSKCVEQPELKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLK
KKCTSNFLSPEKQNSKSNSHHHHHH

Sequence of entity 2 (N, P), FASTA

>4PO7_2 Neurotensin/neuromedin N (chains N, P)
QLYENKPRRPYIL

Ligands and cofactors

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

Water and common crystallization additives (PG4) are not listed.

Primary citation

Revisiting the structure of the Vps10 domain of human sortilin and its interaction with neurotensin. Quistgaard, E.M., Grftehauge, M.K., Madsen, P. et al. Protein Sci (2014) 23:1291-1300. DOI 10.1002/pro.2512 · 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
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
6X4H 2.9 Å, Sortilin-Progranulin Interaction With Compound 24

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