8FY5: Human TMEM175-LAMP1 full-length complex

Human TMEM175-LAMP1 full-length complex. Determined by electron microscopy at 3.5 Å resolution. Released 28 Jun 2023.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,448
Mol. weight: 201.19 kDa
Released: 28 Jun 2023

Explore 8FY5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FY5 contains 49 α-helices and 16 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: 23 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	1
α-helix	34-49	16
α-helix	52-56	5
α-helix	67-101	35
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	178-189	12
β-strand	255-256	2	3
α-helix	258-273	16
α-helix	275-283	9
α-helix	286-287	2
α-helix	288-294	7
α-helix	299-332	34
β-strand	334	1	4
β-strand	337-338	2	3
α-helix	339-352	14
α-helix	355-363	9
α-helix	369-398	30
α-helix	401-404	4
β-strand	405	1	4
α-helix	407-409	3
α-helix	416-439	24
α-helix	441-443	3
α-helix	444-460	17
α-helix	462-475	14

Chain B: 24 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	5
α-helix	34-49	16
α-helix	52-56	5
α-helix	67-101	35
β-strand	102	1	6
β-strand	105	1	5
α-helix	107-120	14
α-helix	123-132	10
α-helix	137-163	27
α-helix	165-167	3
β-strand	168	1	6
α-helix	170-174	5
α-helix	178-189	12
β-strand	255-256	2	7
α-helix	258-273	16
α-helix	275-283	9
α-helix	286-287	2
α-helix	288-294	7
α-helix	299-332	34
β-strand	334	1	8
β-strand	337-338	2	7
α-helix	339-352	14
α-helix	355-363	9
α-helix	369-371	3
α-helix	372-398	27
α-helix	401-404	4
β-strand	405	1	8
α-helix	407-409	3
α-helix	416-439	24
α-helix	441-443	3
α-helix	444-460	17
α-helix	462-475	14

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	384-409	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endosomal/lysosomal potassium channel TMEM175	A, B	protein	504	Homo sapiens	Q9BSA9 (AlphaFold model)
Lysosome-associated membrane glycoprotein 1	C, D	protein	417	Homo sapiens	P11279 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8FY5_1 Endosomal/lysosomal potassium channel TMEM175 (chains A, B)
MSQPRTPEQALDTPGDCPPGRRDEDAGEGIQCSQRMLSFSDALLSIIATVMILPVTHTEI
SPEQQFDRSVQRLLATRIAVYLMTFLIVTVAWAAHTRLFQVVGKTDDTLALLNLACMMTI
TFLPYTFSLMVTFPDVPLGIFLFCVCVIAIGVVQALIVGYAFHFPHLLSPQIQRSAHRAL
YRRHVLGIVLQGPALCFAAAIFSLFFVPLSYLLMVTVILLPYVSKVTGWCRDRLLGHREP
SAHPVEVFSFDLHEPLSKERVEAFSDGVYAIVATLLILDICEDNVPDPKDVKERFSGSLV
AALSATGPRFLAYFGSFATVGLLWFAHHSLFLHVRKATRAMGLLNTLSLAFVGGLPLAYQ
QTSAFARQPRDELERVRVSCTIIFLASIFQLAMWTTALLHQAETLQPSVWFGGREHVLMF
AKLALYPCASLLAFASTCLLSRFSVGIFHLMQIAVPCAFLLLRLLVGLALATLRVLRGLA
RPEHPPPAPTGQDDPQSQLLPAPC

Sequence of entity 2 (C, D), FASTA

>8FY5_2 Lysosome-associated membrane glycoprotein 1 (chains C, D)
MAAPGSARRPLLLLLLLLLLGLMHCASAAMFMVKNGNGTACIMANFSAAFSVNYDTKSGP
KNMTFDLPSDATVVLNRSSCGKENTSDPSLVIAFGRGHTLTLNFTRNATRYSVQLMSFVY
NLSDTHLFPNASSKEIKTVESITDIRADIDKKYRCVSGTQVHMNNVTVTLHDATIQAYLS
NSSFSRGETRCEQDRPSPTTAPPAPPSPSPSPVPKSPSVDKYNVSGTNGTCLLASMGLQL
NLTYERKDNTTVTRLLNINPNKTSASGSCGAHLVTLELHSEGTTVLLFQFGMNASSSRFF
LQGIQLNTILPDARDPAFKAANGSLRALQATVGNSYKCNAEEHVRVTKAFSVNIFKVWVQ
AFKVEGGQFGSVEECLLDENSMLIPIAVGGALAGLVLIVLIAYLVGRKRSHAGYQTI

Primary citation

Lysosomal LAMP proteins regulate lysosomal pH by direct inhibition of the TMEM175 channel. Zhang, J., Zeng, W., Han, Y. et al. Mol Cell (2023) 83:2524-2539.e7. DOI 10.1016/j.molcel.2023.06.004 · 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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