+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7020 | ||||||||||||||||||||||||||||||
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Title | Human Apo-TRPML3 channel at pH 4.8 | ||||||||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||||||||
Sample |
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Keywords | ion channel / TRP channel / lysosomal / TRANSPORT PROTEIN | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information NAADP-sensitive calcium-release channel activity / inner ear auditory receptor cell differentiation / monoatomic anion channel activity / TRP channels / sodium channel activity / autophagosome membrane / potassium channel activity / locomotory behavior / calcium ion transmembrane transport / calcium channel activity ...NAADP-sensitive calcium-release channel activity / inner ear auditory receptor cell differentiation / monoatomic anion channel activity / TRP channels / sodium channel activity / autophagosome membrane / potassium channel activity / 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 | Homo sapiens (human) | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.65 Å | ||||||||||||||||||||||||||||||
Authors | Zhou X / Li M | ||||||||||||||||||||||||||||||
Funding support | China, United States, 9 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2017 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7020.map.gz | 1.7 MB | EMDB map data format | |
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Header (meta data) | emd-7020-v30.xml emd-7020.xml | 16 KB 16 KB | Display Display | EMDB header |
Images | emd_7020.png | 172 KB | ||
Filedesc metadata | emd-7020.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7020 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7020 | HTTPS FTP |
-Validation report
Summary document | emd_7020_validation.pdf.gz | 380.9 KB | Display | EMDB validaton report |
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Full document | emd_7020_full_validation.pdf.gz | 380.5 KB | Display | |
Data in XML | emd_7020_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | emd_7020_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7020 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7020 | HTTPS FTP |
-Related structure data
Related structure data | 6aygMC 7018C 7019C 6ayeC 6ayfC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7020.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.338 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : human TRPML3 channel at pH 4.8
Entire | Name: human TRPML3 channel at pH 4.8 |
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Components |
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-Supramolecule #1: human TRPML3 channel at pH 4.8
Supramolecule | Name: human TRPML3 channel at pH 4.8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 64.625785 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.0 mg/mL | |||||||||||||||
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Buffer | pH: 4.8 Component:
Details: TRPML3 was purified in HEPES buffer pH 7.4. Sodium acetate pH 4.6 was added before freezing, which made the pH to be 4.8 | |||||||||||||||
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 |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL |
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Output model | PDB-6ayg: |