+Open data
-Basic information
Entry | Database: PDB / ID: 6ayg | ||||||||||||||||||||||||||||||
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Title | Human Apo-TRPML3 channel at pH 4.8 | ||||||||||||||||||||||||||||||
Components | Mucolipin-3 | ||||||||||||||||||||||||||||||
Keywords | TRANSPORT PROTEIN / ion channel / TRP channel / lysosomal | ||||||||||||||||||||||||||||||
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 / early endosome membrane / late endosome membrane / lysosomal membrane / lipid binding / plasma membrane Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.65 Å | ||||||||||||||||||||||||||||||
Authors | Zhou, X. / Li, M. / Su, D. / Jia, Q. / Li, H. / Li, X. / Yang, J. | ||||||||||||||||||||||||||||||
Funding support | China, United States, 9items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ayg.cif.gz | 304.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ayg.ent.gz | 220.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ayg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ayg_validation.pdf.gz | 804.2 KB | Display | wwPDB validaton report |
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Full document | 6ayg_full_validation.pdf.gz | 826.8 KB | Display | |
Data in XML | 6ayg_validation.xml.gz | 46.5 KB | Display | |
Data in CIF | 6ayg_validation.cif.gz | 73.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/6ayg ftp://data.pdbj.org/pub/pdb/validation_reports/ay/6ayg | HTTPS FTP |
-Related structure data
Related structure data | 7020MC 7018C 7019C 6ayeC 6ayfC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 64625.785 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCOLN3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8TDD5 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human TRPML3 channel at pH 4.8 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) | |||||||||||||||||||||||||
Buffer solution | pH: 4.8 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 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil holey carbon grid R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Width: 7676 / Height: 7420 / Movie frames/image: 32 / Used frames/image: 1-32 |
-Processing
EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42559 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: RECIPROCAL |