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- EMDB-32083: Structure of Apo-hsTRPM2 channel TM domain -

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Basic information

Entry
Database: EMDB / ID: EMD-32083
TitleStructure of Apo-hsTRPM2 channel TM domain
Map dataTMD-Pore-hsTRPM2-subtract
Sample
  • Cell: TRPM2
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 2
Keywordschannel / trpm2 / Selectivity Filter / TM domain / TRANSPORT PROTEIN
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 / regulation of filopodium assembly / ligand-gated calcium channel activity / cellular response to temperature stimulus / TRP channels ...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 / regulation of filopodium assembly / ligand-gated calcium channel activity / cellular response to temperature stimulus / TRP channels / dendritic cell chemotaxis / sodium channel activity / calcium ion transmembrane import into cytosol / response to hydroperoxide / temperature homeostasis / calcium ion import across plasma membrane / intracellularly gated calcium channel activity / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / monoatomic cation channel activity / release of sequestered calcium ion into cytosol / cellular response to calcium ion / cell projection / regulation of actin cytoskeleton organization / calcium ion transmembrane transport / cytoplasmic vesicle membrane / calcium channel activity / 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
Transient receptor potential cation channel subfamily M member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsYu XF / Xie Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31872796 China
National Natural Science Foundation of China (NSFC)81371302 China
CitationJournal: 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
DepositionOct 18, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0022
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vq2
  • Surface level: 0.0022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32083.png

Downloads & links

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Map

FileDownload / File: emd_32083.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTMD-Pore-hsTRPM2-subtract
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 342. Å		0.86 Å/pix.
x 400 pix.
= 342. Å		0.86 Å/pix.
x 400 pix.
= 342. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0022 / Movie #1: 0.0022
Minimum - Maximum-0.009547057 - 0.017754797
Average (Standard dev.)-0.00007555567 (±0.00028765376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8550.8550.855
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z342.000342.000342.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0100.018-0.000

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Supplemental data

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Sample components

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Entire : TRPM2

EntireName: TRPM2
Components
  • Cell: TRPM2
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 2

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Supramolecule #1: TRPM2

SupramoleculeName: TRPM2 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transient receptor potential cation channel subfamily M member 2

MacromoleculeName: Transient receptor potential cation channel subfamily M member 2
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.967398 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GQLSVDNGLW RVTLCMLAFP LLLTGLISFR EKRLQDVGTP AARARAFFTA PVVVFHLNIL SYFAFLCLFA YVLMVDFQPV PSWCECAIY LWLFSLVCEE MRQLFYDPDE CGLMKKAALY FSDFWNKLDV GAILLFVAGL TCRLIPATLY PGRVILSLDF I LFCLRLMH ...String:
GQLSVDNGLW RVTLCMLAFP LLLTGLISFR EKRLQDVGTP AARARAFFTA PVVVFHLNIL SYFAFLCLFA YVLMVDFQPV PSWCECAIY LWLFSLVCEE MRQLFYDPDE CGLMKKAALY FSDFWNKLDV GAILLFVAGL TCRLIPATLY PGRVILSLDF I LFCLRLMH IFTISKTLGP KIIIVKRMMK DVFFFLFLLA VWVVSFGVAK QAILIHNERR VDWLFRGAVY HSYLTIFGQI PG YIDGVNF NPEHCSPNGT DPYKPKCPES DATQQRPAFP EWLTVLLLCL YLLFTNILLL NLLIAMFNYT FQQVQEHTDQ IWK FQRHDL IEEYHGRPAA PPPFILLSHL QLFIKRVV

UniProtKB: Transient receptor potential cation channel subfamily M member 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68530
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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