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- EMDB-40866: NUDT9-H domain focused cryo-EM map of TRPM2 chanzyme in the prese... -
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Open data
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Basic information
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Title | NUDT9-H domain focused cryo-EM map of TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosphate, and Ribose-5-phosphate | |||||||||||||||
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![]() | TRPM2 Chanzyme / Channel-enzyme / MEMBRANE PROTEIN | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
![]() | Huang Y / Kumar S / Lu W / Du J | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution. Authors: Yihe Huang / Sushant Kumar / Junuk Lee / Wei Lü / Juan Du / ![]() Abstract: Channel enzymes represent a class of ion channels with enzymatic activity directly or indirectly linked to their channel function. We investigated a TRPM2 chanzyme from choanoflagellates that ...Channel enzymes represent a class of ion channels with enzymatic activity directly or indirectly linked to their channel function. We investigated a TRPM2 chanzyme from choanoflagellates that integrates two seemingly incompatible functions into a single peptide: a channel module activated by ADP-ribose with high open probability and an enzyme module (NUDT9-H domain) consuming ADP-ribose at a remarkably slow rate. Using time-resolved cryogenic-electron microscopy, we captured a complete series of structural snapshots of gating and catalytic cycles, revealing the coupling mechanism between channel gating and enzymatic activity. The slow kinetics of the NUDT9-H enzyme module confers a self-regulatory mechanism: ADPR binding triggers NUDT9-H tetramerization, promoting channel opening, while subsequent hydrolysis reduces local ADPR, inducing channel closure. We further demonstrated how the NUDT9-H domain has evolved from a structurally semi-independent ADP-ribose hydrolase module in early species to a fully integrated component of a gating ring essential for channel activation in advanced species. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 258.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.6 KB 16.6 KB | Display Display | ![]() |
Images | ![]() | 67.9 KB | ||
Filedesc metadata | ![]() | 4.8 KB | ||
Others | ![]() ![]() ![]() | 21.5 MB 259.6 MB 259.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 660.4 KB | Display | ![]() |
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Full document | ![]() | 659.9 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.826 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_40866_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40866_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40866_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosph...
Entire | Name: TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosphate, and Ribose-5-phosphate |
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Components |
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-Supramolecule #1: TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosph...
Supramolecule | Name: TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosphate, and Ribose-5-phosphate type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: TRPM2 chanzyme
Macromolecule | Name: TRPM2 chanzyme / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: NRL NSAVAV HGHTAEAAEW YVPPEEYPKS GGVKRYLIDA SMVPLSIMCP SYDPVEYTHP SVAAQPVWAD PADPRKIKFN VKDE VNGKV VDRTSCHPSG ISIDSNTGRP INPWGRTGMT GRGLLGKWGV NQAADTVVTR WKRSPDGSIL ERDGKKVLEF VAIQR QDNK ...String: NRL NSAVAV HGHTAEAAEW YVPPEEYPKS GGVKRYLIDA SMVPLSIMCP SYDPVEYTHP SVAAQPVWAD PADPRKIKFN VKDE VNGKV VDRTSCHPSG ISIDSNTGRP INPWGRTGMT GRGLLGKWGV NQAADTVVTR WKRSPDGSIL ERDGKKVLEF VAIQR QDNK MWAIPGGFVD NGEDVALTSG REFMEEALGM GTSADLMSAE SKDSLAALFS SGTIVARIYC EDPRNTDNAW VETTCV NFH DESGRHAARL KLQGGDDAEH ARWMMVHGGL NLFASHRTLL QHVTSALNAY F(RP5)(AMP)(MG)(MG) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 8.5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.02 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 952710 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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