8T8R: Sortilin-PGRN peptide complex

Sortilin-PGRN peptide complex. Determined by X-ray diffraction at 2.87 Å resolution. Released 26 Jun 2024.

Method: X-ray diffraction
Resolution: 2.87 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,316
Mol. weight: 79.33 kDa
Ligands: NAG
Released: 26 Jun 2024

Explore 8T8R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T8R contains 19 α-helices and 65 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, 63 β-strands

Element	Residues	Length	Sheet
α-helix	60-64	5
β-strand	67-68	2	1
β-strand	71-74	4	1
β-strand	80	1	2
β-strand	81-84	4	3
β-strand	90-97	8	3
β-strand	108-114	7	3
β-strand	122-123	2	3
α-helix	126-128	3
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	175-178	4	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	225-228	4	7
α-helix	230-232	3
β-strand	234-238	5	7
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	372-373	2	8
β-strand	381-386	6	8
β-strand	392-397	6	8
β-strand	405-406	2	8
β-strand	407-408	2	9
α-helix	409-410	2
β-strand	426-430	5	9
α-helix	432-436	5
β-strand	446	1	9
β-strand	455-462	8	9
β-strand	471-475	5	9
β-strand	483-486	4	9
β-strand	490-495	6	10
β-strand	500-505	6	10
β-strand	511	1	11
β-strand	513-517	5	10
β-strand	525-528	4	10
β-strand	534	1	11
β-strand	535-540	6	1
β-strand	549-555	7	1
β-strand	563-570	8	1
β-strand	578	1	12
α-helix	579	1
β-strand	584-588	5	13
β-strand	602	1	13
β-strand	605-612	8	13
β-strand	619	1	12
β-strand	628-632	5	13
α-helix	633	1
β-strand	634	1	14
α-helix	635	1
α-helix	637-639	3
β-strand	640-641	2	15
α-helix	642	1
β-strand	646-647	2	16
β-strand	656-657	2	16
α-helix	664-670	7
α-helix	674-677	4
β-strand	678-679	2	17
β-strand	683-684	2	15
α-helix	685	1
β-strand	691	1	14
α-helix	698-700	3
β-strand	701-702	2	17
α-helix	703-709	7
α-helix	712-714	3

Chain B: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	2
β-strand	15	1	8

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>8T8R_1 Sortilin (chains A)
APGEDEECGRVRDFVAKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVPLVIMT
FGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRIF
RSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVCL
AKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASVM
ADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIFT
SDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRWT
HLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDAI
SVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCWQ
TYTFTRDPIYFTGLASEPGARSMNISIWGFTESFLTSQWVSYTIDFKDILERNCEEKDYT
IWLAHSTDPEDYEDGCILGYKEQFLRLRKSSVCQNGRDYVVTKQPSICLCSLEDFLCDFG
YYRPENDSKCVEQPELKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLKK
KCTSNFLSPEKQNSKSNS

Sequence of entity 2 (B), FASTA

>8T8R_2 Paragranulin peptide (chains B)
PRWDAPLRDPALRPIL

Ligands and cofactors

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

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
6X48 2.9 Å, Sortilin-Progranulin Interaction With Compound 17
6X4H 2.9 Å, Sortilin-Progranulin Interaction With Compound 24

Browse structure collections

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