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- EMDB-7999: Structure of TRPM2 ion channel receptor by single particle electr... -

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Basic information

Entry
Database: EMDB / ID: 7999
TitleStructure of TRPM2 ion channel receptor by single particle electron cryo-microscopy, ADPR/Ca2+ bound state
Map dataIon channel receptor
SampleIon channel 1
  • Transient receptor potential cation channel, subfamily M, member 2
  • (ligand) x 2
Function / homologyun:a0a0r4in04:
Function and homology information
SourceDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsDu J / Lu W / Huang Y / Winkler P / Sun W
CitationJournal: Nature / Year: 2018
Title: Architecture of the TRPM2 channel and its activation mechanism by ADP-ribose and calcium.
Authors: Yihe Huang / Paige A Winkler / Weinan Sun / Wei Lü / Juan Du
Validation ReportPDB-ID: 6drj

SummaryFull reportAbout validation report
DateDeposition: Jun 12, 2018 / Header (metadata) release: Jul 18, 2018 / Map release: Sep 19, 2018 / Last update: Oct 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6drj
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7999.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.07 Å/pix.
= 322.2 Å
300 pix
1.07 Å/pix.
= 322.2 Å
300 pix
1.07 Å/pix.
= 322.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density
Contour Level:3.0 (by author), 3 (movie #1):
Minimum - Maximum-10.673214 - 21.085353999999999
Average (Standard dev.)0.031051211 (0.7776872)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.00.00.0
Limit299.0299.0299.0
Spacing300300300
CellA=B=C: 322.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z322.200322.200322.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-10.67321.0850.031

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Supplemental data

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Sample components

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Entire Ion channel 1

EntireName: Ion channel 1 / Number of components: 4

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Component #1: protein, Ion channel 1

ProteinName: Ion channel 1 / Recombinant expression: No
MassExperimental: 500 kDa
SourceSpecies: Danio rerio (zebrafish)
Source (engineered)Expression System: Mammalia (mammals)

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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: 168.601672 kDa
SourceSpecies: Danio rerio (zebrafish)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, ADENOSINE-5-DIPHOSPHORIBOSE

LigandName: ADENOSINE-5-DIPHOSPHORIBOSE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.559316 kDa

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Component #4: 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: 8
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: 45 e/Å2 / Illumination mode: OTHER
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: 227007
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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