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- EMDB-7822: Cryo-EM structure of the zebrafish TRPM2 channel in the presence ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7822
TitleCryo-EM structure of the zebrafish TRPM2 channel in the presence of Ca2+M2
Map data
SampleTransient receptor potential cation channel subfamily M member 2 (TRPM2)
  • Transient receptor potential cation channel, subfamily M
  • ligand
SourceDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYin Y / Wu M / Borschel WF / Lander GC / Lee S-Y
CitationJournal: To Be Published
Title: Structure of the warmth- and redox-sensing ion channel TRPM2
Authors: Yin Y / Wu M / Borschel WF / Lander GC / Lee S-Y
Validation ReportPDB-ID: 6d73

SummaryFull reportAbout validation report
DateDeposition: Apr 23, 2018 / Header (metadata) release: Jun 13, 2018 / Map release: May 15, 2019 / Update: May 15, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6d73
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_7822.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 320 pix.
= 368. Å
1.15 Å/pix.
x 320 pix.
= 368. Å
1.15 Å/pix.
x 320 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.061772756 - 0.13455923
Average (Standard dev.)0.00055624865 (±0.00646365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0-3200
Dimensions320320320
Spacing320320320
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z368.000368.000368.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS-32000
NC/NR/NS320320320
D min/max/mean-0.0620.1350.001

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Supplemental data

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Sample components

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Entire Transient receptor potential cation channel subfamily M member 2 ...

EntireName: Transient receptor potential cation channel subfamily M member 2 (TRPM2)
Number of components: 3

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Component #1: protein, Transient receptor potential cation channel subfamily M ...

ProteinName: Transient receptor potential cation channel subfamily M member 2 (TRPM2)
Recombinant expression: No
SourceSpecies: Danio rerio (zebrafish)
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
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 167.608625 kDa
SourceSpecies: Danio rerio (zebrafish)
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 solutionSpecimen conc.: 0.5 mg/mL / pH: 8
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 63 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 36000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 2000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3039 / Sampling size: 5 µm

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 93573
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL / Overall bvalue: 100
Output model

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