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- EMDB-43259: 2-PPA bound human TMEM175 -

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Basic information

Entry
Database: EMDB / ID: EMD-43259
Title2-PPA bound human TMEM175
Map data2-PPA bound human TMEM175
Sample
  • Complex: human TMEM175 in an inhibitor-bound state
    • Protein or peptide: Endosomal/lysosomal potassium channel TMEM175
  • Ligand: 2-phenylpyridin-4-amine
KeywordsIon Channel / Lysosome / Potassium Channel / TRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


lysosomal lumen pH elevation / phagosome-lysosome fusion / regulation of lysosomal lumen pH / potassium ion leak channel activity / proton channel activity / arachidonate binding / potassium channel activity / potassium ion transmembrane transport / proton transmembrane transport / neuron cellular homeostasis ...lysosomal lumen pH elevation / phagosome-lysosome fusion / regulation of lysosomal lumen pH / potassium ion leak channel activity / proton channel activity / arachidonate binding / potassium channel activity / potassium ion transmembrane transport / proton transmembrane transport / neuron cellular homeostasis / lysosome / endosome membrane / endosome / lysosomal membrane
Similarity search - Function
Endosomal/lysomomal potassium channel TMEM175 / Endosomal/lysosomal potassium channel TMEM175
Similarity search - Domain/homology
Endosomal/lysosomal proton channel TMEM175
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsOh S / Hite RK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA008748 United States
CitationJournal: To Be Published
Title: Structure of human TMEM175 in an inhibitor-bound state
Authors: Oh S / Hite RK
History
DepositionJan 4, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_43259.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2-PPA bound human TMEM175
Voxel sizeX=Y=Z: 1.064 Å
Density
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-13.470389000000001 - 21.793571
Average (Standard dev.)0.000000000012517 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin818569
Dimensions9587119
Spacing1199587
CellA: 126.616005 Å / B: 101.08 Å / C: 92.568 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : human TMEM175 in an inhibitor-bound state

EntireName: human TMEM175 in an inhibitor-bound state
Components
  • Complex: human TMEM175 in an inhibitor-bound state
    • Protein or peptide: Endosomal/lysosomal potassium channel TMEM175
  • Ligand: 2-phenylpyridin-4-amine

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Supramolecule #1: human TMEM175 in an inhibitor-bound state

SupramoleculeName: human TMEM175 in an inhibitor-bound state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: 2-PPA bound TMEM175
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55 kDa/nm

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Macromolecule #1: Endosomal/lysosomal potassium channel TMEM175

MacromoleculeName: Endosomal/lysosomal potassium channel TMEM175 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.667219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSQPRTPEQA LDTPGDCPPG RRDEDAGEGI QCSQRMLSFS DALLSIIATV MILPVTHTEI SPEQQFDRSV QRLLATRIAV YLMTFLIVT VAWAAHTRLF QVVGKTDDTL ALLNLACMMT ITFLPYTFSL MVTFPDVPLG IFLFCVCVIA IGVVQALIVG Y AFHFPHLL ...String:
MSQPRTPEQA LDTPGDCPPG RRDEDAGEGI QCSQRMLSFS DALLSIIATV MILPVTHTEI SPEQQFDRSV QRLLATRIAV YLMTFLIVT VAWAAHTRLF QVVGKTDDTL ALLNLACMMT ITFLPYTFSL MVTFPDVPLG IFLFCVCVIA IGVVQALIVG Y AFHFPHLL SPQIQRSAHR ALYRRHVLGI VLQGPALCFA AAIFSLFFVP LSYLLMVTVI LLPYVSKVTG WCRDRLLGHR EP SAHPVEV FSFDLHEPLS KERVEAFSDG VYAIVATLLI LDICEDNVPD PKDVKERFSG SLVAALSATG PRFLAYFGSF ATV GLLWFA HHSLFLHVRK ATRAMGLLNT LSLAFVGGLP LAYQQTSAFA RQPRDELERV RVSCTIIFLA SIFQLAMWTT ALLH QAETL QPSVWFGGRE HVLMFAKLAL YPCASLLAFA STCLLSRFSV GIFHLMQIAV PCAFLLLRLL VGLALATLRV LRGLA RPEH PPPAPTGQDD PQSQLLPAPC

UniProtKB: Endosomal/lysosomal proton channel TMEM175

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Macromolecule #2: 2-phenylpyridin-4-amine

MacromoleculeName: 2-phenylpyridin-4-amine / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1AB0
Molecular weightTheoretical: 170.21 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
0.1 %lauryl maltose neopentyl glycol
50.0 mMTris pH 8.0
150.0 mMPotassium ChlorideKCl
2.0 mMDithiothreitol
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 4 seconds prior to plunging.
DetailsDimeric channels

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Average exposure time: 8.0 sec. / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3547408
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wc9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Number images used: 198393
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.12)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 2.12)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Target criteria: FSC
Output model

PDB-8vie:
2-PPA bound human TMEM175

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