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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7018 | ||||||||||||||||||||||||||||||
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Title | Human apo-TRPML3 channel at pH 7.4 | ||||||||||||||||||||||||||||||
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![]() | ion channel / TRP channel / lysosomal / TRANSPORT PROTEIN | ||||||||||||||||||||||||||||||
Function / homology | ![]() NAADP-sensitive calcium-release channel activity / inner ear auditory receptor cell differentiation / TRP channels / autophagosome membrane / locomotory behavior / calcium ion transmembrane transport / calcium channel activity / late endosome membrane / early endosome membrane / lysosomal membrane ...NAADP-sensitive calcium-release channel activity / inner ear auditory receptor cell differentiation / TRP channels / autophagosome membrane / locomotory behavior / calcium ion transmembrane transport / calcium channel activity / late endosome membrane / early endosome membrane / lysosomal membrane / lipid binding / plasma membrane Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.06 Å | ||||||||||||||||||||||||||||||
![]() | Zhou X / Li M | ||||||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states. Authors: Xiaoyuan Zhou / Minghui Li / Deyuan Su / Qi Jia / Huan Li / Xueming Li / Jian Yang / ![]() ![]() Abstract: TRPML3 channels are mainly localized to endolysosomes and play a critical role in the endocytic pathway. Their dysfunction causes deafness and pigmentation defects in mice. TRPML3 activity is ...TRPML3 channels are mainly localized to endolysosomes and play a critical role in the endocytic pathway. Their dysfunction causes deafness and pigmentation defects in mice. TRPML3 activity is inhibited by low endolysosomal pH. Here we present cryo-electron microscopy (cryo-EM) structures of human TRPML3 in the closed, agonist-activated, and low-pH-inhibited states, with resolutions of 4.06, 3.62, and 4.65 Å, respectively. The agonist ML-SA1 lodges between S5 and S6 and opens an S6 gate. A polycystin-mucolipin domain (PMD) forms a luminal cap. S1 extends into this cap, forming a 'gating rod' that connects directly to a luminal pore loop, which undergoes dramatic conformational changes in response to low pH. S2 extends intracellularly and interacts with several intracellular regions to form a 'gating knob'. These unique structural features, combined with the results of electrophysiological studies, indicate a new mechanism by which luminal pH and other physiological modulators such as PIP regulate TRPML3 by changing S1 and S2 conformations. | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.4 KB 15.4 KB | Display Display | ![]() |
Images | ![]() | 89.3 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 398 KB | Display | ![]() |
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Full document | ![]() | 397.6 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ayeMC ![]() 7019C ![]() 7020C ![]() 6ayfC ![]() 6aygC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : human TRPML3 apo channel at pH 7.4
Entire | Name: human TRPML3 apo channel at pH 7.4 |
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Components |
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-Supramolecule #1: human TRPML3 apo channel at pH 7.4
Supramolecule | Name: human TRPML3 apo channel at pH 7.4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Mucolipin-3
Macromolecule | Name: Mucolipin-3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 64.625785 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GGGGSMADPE VVVSSCSSHE EENRCNFNQQ TSPSEELLLE DQMRRKLKFF FMNPCEKFWA RGRKPWKLAI QILKIAMVTI QLVLFGLSN QMVVAFKEEN TIAFKHLFLK GYMDRMDDTY AVYTQSDVYD QLIFAVNQYL QLYNVSVGNH AYENKGTKQS A MAICQHFY ...String: GGGGSMADPE VVVSSCSSHE EENRCNFNQQ TSPSEELLLE DQMRRKLKFF FMNPCEKFWA RGRKPWKLAI QILKIAMVTI QLVLFGLSN QMVVAFKEEN TIAFKHLFLK GYMDRMDDTY AVYTQSDVYD QLIFAVNQYL QLYNVSVGNH AYENKGTKQS A MAICQHFY KRGNIYPGND TFDIDPEIET ECFFVEPDEP FHIGTPAENK LNLTLDFHRL LTVELQFKLK AINLQTVRHQ EL PDCYDFT LTITFDNKAH SGRIKISLDN DISIRECKDW HVSGSIQKNT HYMMIFDAFV ILTCLVSLIL CIRSVIRGLQ LQQ EFVNFF LLHYKKEVSV SDQMEFVNGW YIMIIISDIL TIIGSILKME IQAKSLTSYD VCSILLGTST MLVWLGVIRY LGFF AKYNL LILTLQAALP NVIRFCCCAA MIYLGYCFCG WIVLGPYHDK FRSLNMVSEC LFSLINGDDM FATFAKMQQK SYLVW LFSR IYLYSFISLF IYMILSLFIA LITDTYETIK QYQQDGFPET ELRTFISECK DLPNSGKYRL EDDPPVSLFC CCKK UniProtKB: Mucolipin-3 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.9 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: The pH of the buffer was adjusted to 7.4 by NaOH. | |||||||||
Grid | Model: Quantifoil holey carbon grid R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV Details: waiting for 3 seconds before blotting for 4 seconds(double-sided, blot force 1),then the grid was immediately plunged into liquid ethane cooled by liquid-nitrogen. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 1-32 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |