- EMDB-32083: Structure of Apo-hsTRPM2 channel TM domain -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-32083
Title
Structure of Apo-hsTRPM2 channel TM domain
Map data
TMD-Pore-hsTRPM2-subtract
Sample
Cell: TRPM2
Protein or peptide: Transient receptor potential cation channel subfamily M member 2
Function / homology
Function and homology information
cellular response to purine-containing compound / mono-ADP-D-ribose binding / manganese ion transmembrane transporter activity / zinc ion transmembrane transport / dendritic cell differentiation / response to purine-containing compound / ligand-gated calcium channel activity / regulation of filopodium assembly / cellular response to temperature stimulus / sodium channel activity ...cellular response to purine-containing compound / mono-ADP-D-ribose binding / manganese ion transmembrane transporter activity / zinc ion transmembrane transport / dendritic cell differentiation / response to purine-containing compound / ligand-gated calcium channel activity / regulation of filopodium assembly / cellular response to temperature stimulus / sodium channel activity / TRP channels / response to hydroperoxide / calcium ion transmembrane import into cytosol / dendritic cell chemotaxis / temperature homeostasis / intracellularly gated calcium channel activity / tertiary granule membrane / : / ficolin-1-rich granule membrane / calcium ion import across plasma membrane / monoatomic cation channel activity / specific granule membrane / release of sequestered calcium ion into cytosol / cellular response to calcium ion / cell projection / regulation of actin cytoskeleton organization / calcium ion transmembrane transport / calcium channel activity / cytoplasmic vesicle membrane / cellular response to hydrogen peroxide / calcium ion transport / response to heat / perikaryon / protein homotetramerization / lysosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / plasma membrane Similarity search - Function
TRPM, SLOG domain / SLOG in TRPM / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Ion transport domain / Ion transport protein Similarity search - Domain/homology
National Natural Science Foundation of China (NSFC)
31872796
China
National Natural Science Foundation of China (NSFC)
81371302
China
Citation
Journal: Cell Rep / Year: 2021 Title: Structural and functional basis of the selectivity filter as a gate in human TRPM2 channel. Authors: Xiafei Yu / Yuan Xie / Xiaokang Zhang / Cheng Ma / Likun Liu / Wenxuan Zhen / Lingyi Xu / Jianmin Zhang / Yan Liang / Lixia Zhao / Xiuxia Gao / Peilin Yu / Jianhong Luo / Lin-Hua Jiang / Yan ...Authors: Xiafei Yu / Yuan Xie / Xiaokang Zhang / Cheng Ma / Likun Liu / Wenxuan Zhen / Lingyi Xu / Jianmin Zhang / Yan Liang / Lixia Zhao / Xiuxia Gao / Peilin Yu / Jianhong Luo / Lin-Hua Jiang / Yan Nie / Fan Yang / Jiangtao Guo / Wei Yang / Abstract: Transient receptor potential melastatin 2 (TRPM2), a Ca-permeable cation channel, is gated by intracellular adenosine diphosphate ribose (ADPR), Ca, warm temperature, and oxidative stress. It is ...Transient receptor potential melastatin 2 (TRPM2), a Ca-permeable cation channel, is gated by intracellular adenosine diphosphate ribose (ADPR), Ca, warm temperature, and oxidative stress. It is critically involved in physiological and pathological processes ranging from inflammation to stroke to neurodegeneration. At present, the channel's gating and ion permeation mechanisms, such as the location and identity of the selectivity filter, remain ambiguous. Here, we report the cryo-electron microscopy (cryo-EM) structure of human TRPM2 in nanodisc in the ligand-free state. Cryo-EM map-guided computational modeling and patch-clamp recording further identify a quadruple-residue motif as the ion selectivity filter, which adopts a restrictive conformation in the closed state and acts as a gate, profoundly contrasting with its widely open conformation in the Nematostella vectensis TRPM2. Our study reveals the gating of human TRPM2 by the filter and demonstrates the feasibility of using cryo-EM in conjunction with computational modeling and functional studies to garner structural information for intrinsically dynamic but functionally important domains.
History
Deposition
Oct 18, 2021
-
Header (metadata) release
Dec 22, 2021
-
Map release
Dec 22, 2021
-
Update
Dec 22, 2021
-
Current status
Dec 22, 2021
Processing site: PDBj / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi