8T8S: Sortilin-PGRN peptide complex

Sortilin-PGRN peptide complex. Determined by X-ray diffraction at 2.99 Å resolution. Released 26 Jun 2024.

Method: X-ray diffraction
Resolution: 2.99 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,691
Mol. weight: 158.17 kDa
Ligands: NAG
Released: 26 Jun 2024

Explore 8T8S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T8S contains 48 α-helices and 128 β-strands across 4 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, 62 β-strands

Element	Residues	Length	Sheet
α-helix	59-64	6
β-strand	67-74	8	1
β-strand	78	1	2
β-strand	79-80	2	3
β-strand	81-83	3	2
β-strand	91-99	9	2
β-strand	106-114	9	2
β-strand	121-123	3	2
α-helix	125-128	4
β-strand	133	1	4
β-strand	140-141	2	4
α-helix	142	1
β-strand	149-153	5	4
β-strand	163-167	5	4
β-strand	174-178	5	4
β-strand	183	1	5
β-strand	188-189	2	6
α-helix	190	1
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
α-helix	230-232	3
β-strand	234-238	5	7
α-helix	244-247	4
β-strand	251-256	6	7
β-strand	264-276	13	7
β-strand	279-285	7	7
α-helix	286	1
β-strand	292-297	6	7
β-strand	305-306	2	7
β-strand	312	1	7
β-strand	318-323	6	8
β-strand	328-333	6	8
α-helix	334	1
β-strand	340-346	7	8
β-strand	353-361	9	8
β-strand	362	1	9
β-strand	369	1	9
β-strand	372-373	2	8
β-strand	381-386	6	8
β-strand	392-397	6	8
β-strand	404-406	3	8
β-strand	407-408	2	10
α-helix	409-410	2
β-strand	426-429	4	10
α-helix	432-436	5
β-strand	446-447	2	10
β-strand	455-462	8	10
α-helix	469-470	2
β-strand	471-475	5	10
β-strand	483-486	4	10
β-strand	490-495	6	11
α-helix	496-498	3
β-strand	500-505	6	11
β-strand	511	1	1
β-strand	513-517	5	11
β-strand	525-528	4	11
β-strand	534-541	8	1
β-strand	549-556	8	1
β-strand	563-570	8	1
β-strand	578	1	12
α-helix	579	1
α-helix	581-583	3
β-strand	584-588	5	13
β-strand	602	1	13
β-strand	605-612	8	13
α-helix	613	1
β-strand	619	1	12
β-strand	628-632	5	13
α-helix	633-634	2
β-strand	635	1	14
α-helix	637-639	3
β-strand	640-642	3	15
α-helix	643	1
β-strand	646-647	2	16
β-strand	656-657	2	16
α-helix	664-670	7
β-strand	682-684	3	15
α-helix	685	1
β-strand	693	1	14

Chain B: 26 helices, 62 β-strands

Element	Residues	Length	Sheet
α-helix	55-56	2
α-helix	59-64	6
β-strand	67-71	5	17
α-helix	75	1
β-strand	78-83	6	18
β-strand	91-99	9	18
β-strand	106-113	8	18
β-strand	122-123	2	18
α-helix	125-128	4
β-strand	133	1	19
β-strand	140-141	2	19
α-helix	142	1
β-strand	149-153	5	19
β-strand	163-167	5	19
β-strand	174-178	5	19
β-strand	183	1	20
β-strand	188-189	2	21
α-helix	190	1
β-strand	197-200	4	21
β-strand	201	1	20
β-strand	206-209	4	21
β-strand	217-220	4	21
β-strand	223-228	6	22
α-helix	230-232	3
β-strand	234-238	5	22
α-helix	244-247	4
β-strand	251-256	6	22
β-strand	264-276	13	22
β-strand	279-285	7	22
α-helix	286	1
β-strand	292-297	6	22
β-strand	305-306	2	22
β-strand	312	1	22
β-strand	318-323	6	23
β-strand	328-333	6	23
α-helix	334	1
β-strand	340-346	7	23
β-strand	353-361	9	23
β-strand	362	1	24
β-strand	369	1	24
β-strand	372-373	2	23
β-strand	381-386	6	23
β-strand	392-397	6	23
β-strand	404-406	3	23
β-strand	407-408	2	25
α-helix	409-410	2
β-strand	426-429	4	25
α-helix	432-436	5
β-strand	446	1	25
β-strand	455-462	8	25
α-helix	470	1
β-strand	471-475	5	25
β-strand	483-486	4	25
β-strand	490-495	6	26
α-helix	496-498	3
β-strand	500-505	6	26
β-strand	511	1	17
β-strand	513-517	5	26
β-strand	525-528	4	26
β-strand	534-541	8	17
β-strand	549-556	8	17
β-strand	564-570	7	17
β-strand	578	1	27
α-helix	579	1
α-helix	581-583	3
β-strand	584-588	5	13
β-strand	602	1	13
β-strand	605-612	8	13
α-helix	613	1
β-strand	619	1	27
β-strand	628-632	5	13
α-helix	633-634	2
β-strand	635	1	28
α-helix	637-639	3
β-strand	640-642	3	29
α-helix	643	1
β-strand	646-647	2	30
β-strand	656-657	2	30
α-helix	664-671	8
α-helix	674-677	4
β-strand	678-679	2	31
β-strand	682-684	3	29
α-helix	685	1
β-strand	693	1	28
α-helix	698-700	3
β-strand	701-702	2	31
α-helix	703-709	7
α-helix	712-713	2

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	3
α-helix	12-14	3
β-strand	15	1	8

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	18
α-helix	12-13	2
β-strand	14-15	2	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sortilin	A, B	protein	678	Homo sapiens	Q99523 (AlphaFold model)
Paragranulin peptide	C, D	protein	16	Homo sapiens	P28799 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8T8S_1 Sortilin (chains A, B)
APGEDEECGRVRDFVAKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVPLVIMT
FGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRIF
RSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVCL
AKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASVM
ADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIFT
SDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRWT
HLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDAI
SVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCWQ
TYTFTRDPIYFTGLASEPGARSMNISIWGFTESFLTSQWVSYTIDFKDILERNCEEKDYT
IWLAHSTDPEDYEDGCILGYKEQFLRLRKSSVCQNGRDYVVTKQPSICLCSLEDFLCDFG
YYRPENDSKCVEQPELKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLKK
KCTSNFLSPEKQNSKSNS

Sequence of entity 2 (C, D), FASTA

>8T8S_2 Paragranulin peptide (chains C, D)
PRWDAPLRDPALRQLL

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 (CL) are not listed.

Primary citation

Structural studies of Sortilin-PGRN peptide complex. Srivastava, D.B., Cherf, G.M., Low, L.Y. et al. To be published.

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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