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- PDB-6d73: Cryo-EM structure of the zebrafish TRPM2 channel in the presence ... -

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Entry
Database: PDB / ID: 6d73
TitleCryo-EM structure of the zebrafish TRPM2 channel in the presence of Ca2+M2
ComponentsTransient receptor potential cation channel, subfamily M
KeywordsTRANSPORT PROTEIN / warmth sensor / redox sensor / calcium-permeable ion channel / ion channel
Specimen sourceDanio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYin, Y. / Wu, M. / Borschel, W.F. / Lander, G.C. / Lee, S.-Y.
Funding support1件
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke
CitationJournal: To Be Published
Title: Structure of the warmth- and redox-sensing ion channel TRPM2
Authors: Yin, Y. / Wu, M. / Borschel, W.F. / Lander, G.C. / Lee, S.-Y.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 23, 2018 / Release: May 15, 2019Array

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Assembly

Deposited unit
B: Transient receptor potential cation channel, subfamily M
A: Transient receptor potential cation channel, subfamily M
C: Transient receptor potential cation channel, subfamily M
D: Transient receptor potential cation channel, subfamily M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)670,5958
Polymers670,4354
Non-polymers1604
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Transient receptor potential cation channel, subfamily M


Mass: 167608.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trpm2 / Production host: Homo sapiens (human)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Calcium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Transient receptor potential cation channel subfamily M member 2 (TRPM2)
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Danio rerio (zebrafish)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 36000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 16 sec. / Electron dose: 63 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3039
Image scansSampling size: 5 µns / Width: 3710 / Height: 3838 / Movie frames/image: 64 / Used frames/image: 1-64

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2Leginon3.2image acquisitionAutomated data acquisition software
4CTFFIND4CTF correction
5RELION2.1CTF correction
8Coot0.8.8model fitting
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
13RELION2.13D reconstruction
14PHENIX1.12-2829-000model refinement
15Coot0.8.8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1791114
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93573 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 100 / Protocol: RIGID BODY FIT / Space: REAL
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.00436716
f_angle_d0.68350298
f_dihedral_angle_d8.62421224
f_chiral_restr0.0415948
f_plane_restr0.0056374

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