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- EMDB-9134: Human TRPM2 ion channel in a calcium- and ADPR-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-9134
TitleHuman TRPM2 ion channel in a calcium- and ADPR-bound state
Map data
SampleHuman TRPM2 ion channel
  • Transient receptor potential cation channel subfamily M member 2
  • ligand
Function / homology
Function and homology information


cellular response to purine-containing compound / response to purine-containing compound / mono-ADP-D-ribose binding / zinc ion transmembrane transport / cellular response to temperature stimulus / ligand-gated calcium channel activity / cation transmembrane transport / dendritic cell differentiation / metal ion transport / regulation of filopodium assembly ...cellular response to purine-containing compound / response to purine-containing compound / mono-ADP-D-ribose binding / zinc ion transmembrane transport / cellular response to temperature stimulus / ligand-gated calcium channel activity / cation transmembrane transport / dendritic cell differentiation / metal ion transport / regulation of filopodium assembly / temperature homeostasis / sodium channel activity / calcium ion transmembrane import into cytosol / TRP channels / calcium ion import across plasma membrane / regulation of actin cytoskeleton reorganization / dendritic cell chemotaxis / calcium-release channel activity / ficolin-1-rich granule membrane / tertiary granule membrane / release of sequestered calcium ion into cytosol / calcium-mediated signaling using intracellular calcium source / cation channel activity / specific granule membrane / cellular response to calcium ion / calcium channel activity / calcium ion transmembrane transport / cell projection / calcium ion transport / cellular response to hydrogen peroxide / lysosomal membrane / cytoplasmic vesicle membrane / perikaryon / protein homotetramerization / lysosome / Neutrophil degranulation / neutrophil degranulation / calcium ion binding / integral component of plasma membrane / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily M member 2 / SLOG in TRPM / TRPM, SLOG domain / NUDIX hydrolase domain / Nudix hydrolase domain profile. / 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: 6.36 Å
AuthorsWang L / Fu TM / Xia S / Wu H
CitationJournal: Science / Year: 2018
Title: Structures and gating mechanism of human TRPM2.
Authors: Longfei Wang / Tian-Min Fu / Yiming Zhou / Shiyu Xia / Anna Greka / Hao Wu /
Abstract: Transient receptor potential (TRP) melastatin 2 (TRPM2) is a cation channel associated with numerous diseases. It has a C-terminal NUDT9 homology (NUDT9H) domain responsible for binding adenosine ...Transient receptor potential (TRP) melastatin 2 (TRPM2) is a cation channel associated with numerous diseases. It has a C-terminal NUDT9 homology (NUDT9H) domain responsible for binding adenosine diphosphate (ADP)-ribose (ADPR), and both ADPR and calcium (Ca) are required for TRPM2 activation. Here we report cryo-electron microscopy structures of human TRPM2 alone, with ADPR, and with ADPR and Ca NUDT9H forms both intra- and intersubunit interactions with the N-terminal TRPM homology region (MHR1/2/3) in the apo state but undergoes conformational changes upon ADPR binding, resulting in rotation of MHR1/2 and disruption of the intersubunit interaction. The binding of Ca further engages transmembrane helices and the conserved TRP helix to cause conformational changes at the MHR arm and the lower gating pore to potentiate channel opening. These findings explain the molecular mechanism of concerted TRPM2 gating by ADPR and Ca and provide insights into the gating mechanism of other TRP channels.
History
DepositionSep 20, 2018-
Header (metadata) releaseNov 14, 2018-
Map releaseDec 12, 2018-
UpdateDec 12, 2018-
Current statusDec 12, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.77
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.77
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9134.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å
1.07 Å/pix.
x 300 pix.
= 321. Å
1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 2.77 / Movie #1: 2.77
Minimum - Maximum-13.418454000000001 - 21.981209
Average (Standard dev.)-0.000000000000725 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z321.000321.000321.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-13.41821.981-0.000

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Supplemental data

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Sample components

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Entire Human TRPM2 ion channel

EntireName: Human TRPM2 ion channel / Number of components: 3

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Component #1: protein, Human TRPM2 ion channel

ProteinName: Human TRPM2 ion channel / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Transient receptor potential cation channel subfamily M ...

ProteinName: Transient receptor potential cation channel subfamily M member 2
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 171.416188 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 70.072 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 14199
3D reconstructionResolution: 6.36 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: cisTEM

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Atomic model buiding

Output model

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