+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43257 | |||||||||
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Title | AP-6 bound human TMEM175 | |||||||||
Map data | AP-6 bound TMEM175 | |||||||||
Sample |
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Keywords | Ion Channel / Lysosome / Potassium Channel / TRANSPORT 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
Authors | Oh S / Hite RK | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Structure of human TMEM175 in an inhibitor-bound state Authors: Oh S / Hite RK | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43257.map.gz | 200.6 MB | EMDB map data format | |
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Header (meta data) | emd-43257-v30.xml emd-43257.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_43257.png | 72.5 KB | ||
Filedesc metadata | emd-43257.cif.gz | 6 KB | ||
Others | emd_43257_half_map_1.map.gz emd_43257_half_map_2.map.gz | 200.3 MB 200.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43257 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43257 | HTTPS FTP |
-Related structure data
Related structure data | 8vicMC 8vieC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_43257.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | AP-6 bound TMEM175 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8255 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map A
File | emd_43257_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_43257_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human TMEM175 in an inhibitor-bound state
Entire | Name: human TMEM175 in an inhibitor-bound state |
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Components |
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-Supramolecule #1: human TMEM175 in an inhibitor-bound state
Supramolecule | Name: human TMEM175 in an inhibitor-bound state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: AP-6 bound TMEM175 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55 kDa/nm |
-Macromolecule #1: Endosomal/lysosomal potassium channel TMEM175
Macromolecule | Name: Endosomal/lysosomal potassium channel TMEM175 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.667219 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: (2P,2'P)-2,2'-(1,3-phenylene)di(pyridin-4-amine)
Macromolecule | Name: (2P,2'P)-2,2'-(1,3-phenylene)di(pyridin-4-amine) / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1AA3 |
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Molecular weight | Theoretical: 262.309 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 4 seconds prior to plunging. | |||||||||||||||
Details | Dimeric channels |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 2 / Average exposure time: 3.0 sec. / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Target criteria: FSC |
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Output model | PDB-8vic: |