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Yorodumi- EMDB-40872: NUDT9-H domain focused cryo-EM map of TRPM2 chanzyme (E1114A) in ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40872 | |||||||||||||||
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Title | NUDT9-H domain focused cryo-EM map of TRPM2 chanzyme (E1114A) in the presence of Magnesium and ADP-ribose, closed state | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | TRPM2 Chanzyme / Channel-enzyme / MEMBRANE PROTEIN | |||||||||||||||
Biological species | Salpingoeca rosetta (eukaryote) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.27 Å | |||||||||||||||
Authors | Huang Y / Kumar S / Lu W / Du J | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 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 | emd_40872.map.gz | 258.4 MB | EMDB map data format | |
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Header (meta data) | emd-40872-v30.xml emd-40872.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
Images | emd_40872.png | 53.2 KB | ||
Filedesc metadata | emd-40872.cif.gz | 4.8 KB | ||
Others | emd_40872_additional_1.map.gz emd_40872_half_map_1.map.gz emd_40872_half_map_2.map.gz | 20 MB 258.9 MB 259 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40872 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40872 | HTTPS FTP |
-Validation report
Summary document | emd_40872_validation.pdf.gz | 649.5 KB | Display | EMDB validaton report |
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Full document | emd_40872_full_validation.pdf.gz | 649.1 KB | Display | |
Data in XML | emd_40872_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_40872_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40872 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40872 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40872.map.gz / Format: CCP4 / Size: 325 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: 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_40872_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40872_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40872_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TRPM2 chanzyme (E1114A) incubated with Magnesium and ADP-ribose f...
Entire | Name: TRPM2 chanzyme (E1114A) incubated with Magnesium and ADP-ribose for 5s; ADP-ribose intact; closed state |
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Components |
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-Supramolecule #1: TRPM2 chanzyme (E1114A) incubated with Magnesium and ADP-ribose f...
Supramolecule | Name: TRPM2 chanzyme (E1114A) incubated with Magnesium and ADP-ribose for 5s; ADP-ribose intact; closed state type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Salpingoeca rosetta (eukaryote) |
-Macromolecule #1: TRPM2 chanzyme (E1114A) incubated with Magnesium and ADP-ribose f...
Macromolecule | Name: TRPM2 chanzyme (E1114A) incubated with Magnesium and ADP-ribose for 5s; ADP-ribose intact; closed state type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Salpingoeca rosetta (eukaryote) |
Recombinant expression | Organism: Homo sapiens (human) |
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(MG)(MG)(MG)(APR) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8.5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-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: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 379553 |
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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