9VSP: The DCY1020-bound structure of TMEM175

The DCY1020-bound structure of TMEM175. Determined by electron microscopy at 3.4 Å resolution. Released 17 Sept 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,436
Mol. weight: 112.24 kDa
Ligands: A1ETD
Released: 17 Sept 2025

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

Secondary structure: helices and β-sheets

9VSP contains 45 α-helices and 12 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: 22 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	1
α-helix	33-49	17
α-helix	52-57	6
α-helix	70-101	32
β-strand	102	1	2
β-strand	105	1	1
α-helix	107-120	14
α-helix	123-132	10
α-helix	137-163	27
α-helix	165-167	3
β-strand	168	1	2
α-helix	170-174	5
α-helix	178-203	26
α-helix	207-223	17
α-helix	258-283	26
α-helix	286-287	2
α-helix	288-294	7
α-helix	299-332	34
β-strand	334	1	3
α-helix	339-352	14
α-helix	355-363	9
α-helix	369-399	31
α-helix	401-404	4
β-strand	405	1	3
α-helix	407-409	3
α-helix	416-439	24
α-helix	444-460	17
α-helix	462-474	13

Chain B: 23 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	4
α-helix	34-48	15
α-helix	49-51	3
α-helix	52-57	6
α-helix	70-101	32
β-strand	105	1	4
α-helix	107-120	14
α-helix	123-132	10
α-helix	137-163	27
α-helix	165-167	3
α-helix	170-174	5
α-helix	178-202	25
α-helix	207-223	17
β-strand	255-256	2	5
α-helix	257	1
α-helix	258-283	26
α-helix	286-287	2
α-helix	288-294	7
α-helix	299-332	34
β-strand	334	1	6
β-strand	337-338	2	5
α-helix	339-352	14
α-helix	355-363	9
α-helix	369-398	30
α-helix	401-404	4
β-strand	405	1	6
α-helix	407-409	3
α-helix	416-439	24
α-helix	444-475	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endosomal/lysosomal proton channel TMEM175	A, B	protein	504	Homo sapiens	Q9BSA9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9VSP_1 Endosomal/lysosomal proton channel TMEM175 (chains A, B)
MSQPRTPEQALDTPGDCPPGRRDEDAGEGIQCSQRMLSFSDALLSIIATVMILPVTHTEI
SPEQQFDRSVQRLLATRIAVYLMTFLIVTVAWAAHTRLFQVVGKTDDTLALLNLACMMTI
TFLPYTFSLMVTFPDVPLGIFLFCVCVIAIGVVQALIVGYAFHFPHLLSPQIQRSAHRAL
YRRHVLGIVLQGPALCFAAAIFSLFFVPLSYLLMVTVILLPYVSKVTGWCRDRLLGHREP
SAHPVEVFSFDLHEPLSKERVEAFSDGVYAIVATLLILDICEDNVPDPKDVKERFSGSLV
AALSATGPRFLAYFGSFATVGLLWFAHHSLFLHVRKATRAMGLLNTLSLAFVGGLPLAYQ
QTSAFARQPRDELERVRVSCTIIFLASIFQLAMWTTALLHQAETLQPSVWFGGREHVLMF
AKLALYPCASLLAFASTCLLSRFSVGIFHLMQIAVPCAFLLLRLLVGLALATLRVLRGLA
RPEHPPPAPTGQDDPQSQLLPAPC

Ligands and cofactors

ID	Name	Formula	Copies
A1ETD	(2S)-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-5-[3-(1H-1,2,3,4-tetrazol-5-yl)pr…	C22 H28 Cl2 N4 O2	2

Primary citation

Structural insights into the activation of TMEM175 by small molecule. Zhu, X., Ping, M., Liu, H. et al. Neuron (2025) 113:3567. DOI 10.1016/j.neuron.2025.07.029 · PubMed

Other PDB entries of the same protein (UniProt Q9BSA9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7UNL 2.45 Å, Human TMEM175 in an open state
7UNM 2.61 Å, Human TMEM175 in an closed state
6WC9 2.64 Å, Human open state TMEM175 in KCl
8DHM 2.73 Å, Human TMEM175 in complex with 4-aminopyridine
9VSQ 2.74 Å, The TUG-891-bound structure of TMEM175
9VSR 2.92 Å, The DCY1040 and TUG-891-bound structure of TMEM175
6WCA 3.03 Å, Human closed state TMEM175 in KCl
6WCB 3.17 Å, Human open state TMEM175 in CsCl
6W8N 3.2 Å, Structure of a trans-membrane protein
6WCC 3.24 Å, Human closed state TMEM175 in CsCl
6W8O 3.4 Å, Structure of an Apo membrane protein
8FYF 3.4 Å, Human TMEM175-LAMP1 transmembrane domain only complex

Browse structure collections

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