6EHO: Dimer of the Sortilin Vps10p domain at low pH

Dimer of the Sortilin Vps10p domain at low pH. Determined by X-ray diffraction at 3.5 Å resolution. Released 6 Dec 2017.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 1
Atoms: 5,163
Mol. weight: 82.3 kDa
Released: 6 Dec 2017

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

Secondary structure: helices and β-sheets

6EHO contains 15 α-helices and 59 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: 15 helices, 59 β-strands

Element	Residues	Length	Sheet
α-helix	60-66	7
β-strand	68-73	6	1
β-strand	78-83	6	2
β-strand	91-97	7	2
β-strand	111-114	4	2
β-strand	122-123	2	2
β-strand	131-134	4	2
β-strand	139-141	3	3
α-helix	144-146	3
β-strand	149-152	4	3
β-strand	153-155	3	2
β-strand	163-167	5	3
β-strand	174-178	5	3
β-strand	183	1	4
β-strand	188-189	2	5
β-strand	197-200	4	5
β-strand	201	1	4
β-strand	206-209	4	5
β-strand	216-220	5	5
β-strand	223-228	6	6
β-strand	234-238	5	6
α-helix	245-247	3
β-strand	252-256	5	6
β-strand	264-268	5	6
β-strand	273-274	2	7
β-strand	280-283	4	7
β-strand	294-297	4	7
α-helix	305	1
β-strand	306	1	7
α-helix	307	1
β-strand	308	1	8
β-strand	318-323	6	9
β-strand	328-333	6	9
α-helix	334	1
β-strand	340-345	6	9
β-strand	352	1	8
β-strand	354-361	8	9
β-strand	372-374	3	9
β-strand	380-385	6	9
β-strand	393-397	5	9
β-strand	404-406	3	9
α-helix	407-410	4
α-helix	432-436	5
β-strand	446	1	10
β-strand	455-458	4	10
α-helix	464-468	5
β-strand	472-475	4	10
β-strand	483-486	4	10
β-strand	490-495	6	11
α-helix	496-498	3
β-strand	500-505	6	11
α-helix	510	1
β-strand	511	1	1
β-strand	513-517	5	11
β-strand	524-528	5	11
β-strand	534-541	8	1
β-strand	549-556	8	1
β-strand	564-570	7	1
β-strand	578	1	12
α-helix	581-583	3
β-strand	584-588	5	13
β-strand	601-602	2	14
β-strand	605-606	2	14
β-strand	608-612	5	13
α-helix	613	1
β-strand	619	1	12
β-strand	625	1	13
α-helix	630	1
β-strand	631-632	2	14
α-helix	633-635	3
β-strand	640-641	2	15
β-strand	646-647	2	16
β-strand	656-657	2	16
β-strand	683-684	2	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sortilin	A	protein	723	Homo sapiens	Q99523 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6EHO_1 Sortilin (chains A)
QDRLDAPPPPAAPLPRWSGPIGVSWGLRAAAAGGAFPRGGRWGGSAPGEDEECGRVRDFV
AKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVPLVIMTFGQSKLYRSEDYGKN
FKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRIFRSSDFAKNFVQTDLP
FHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVCLAKWGSDNTIFFTTYA
NGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASVMADKDTTRRIHVSTDQ
GDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIFTSDDRGIVYSKSLDRH
LYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRWTHLRKPENSECDATAK
NKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDAISVMVPDVYISDDGGY
SWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCWQTYTFTRDPIYFTGLA
SEPGARSMNISIWGFTESFLTSQWVSYTIDFKDILERNCEEKDYTIWLAHSTDPEDYEDG
CILGYKEQFLRLRKSSMCQNGRDYVVTKQPSICLCSLEDFLCDFGYYRPENDSKCVEQPE
LKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLKKKCTSNFLSPEKQNSK
SNS

Primary citation

Acidic Environment Induces Dimerization and Ligand Binding Site Collapse in the Vps10p Domain of Sortilin. Januliene, D., Andersen, J.L., Nielsen, J.A. et al. Structure (2017) 25:1809-1819.e3. DOI 10.1016/j.str.2017.09.015 · 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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