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- PDB-5ydz: structure of endo-lysosomal TRPML1 channel inserting into amphipo... -

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Basic information

Entry
Database: PDB / ID: 5ydz
Titlestructure of endo-lysosomal TRPML1 channel inserting into amphipol: state 1
Descriptorlysosomal protein
KeywordsMEMBRANE PROTEIN / mTRPML1 / mucolipidosis type IV / structual comparisons / combined regulation mechanism
Specimen sourceMus musculus / mammal / Mouse / ハツカネズミ, はつかねずみ /
MethodElectron microscopy (5.8 Å resolution / Particle / Single particle)
AuthorsYang, M. / Gao, N.
CitationProtein Cell, 2017, 8, 834-847

Protein Cell, 2017, 8, 834-847 Yorodumi Papers
Cryo-EM structures of the mammalian endo-lysosomal TRPML1 channel elucidate the combined regulation mechanism.
Sensen Zhang / Ningning Li / Wenwen Zeng / Ning Gao / Maojun Yang

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 15, 2017 / Release: Dec 27, 2017

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Assembly

Deposited unit
A: mammalian endo-lysosomal TRPML1 channel
B: mammalian endo-lysosomal TRPML1 channel
C: mammalian endo-lysosomal TRPML1 channel
D: mammalian endo-lysosomal TRPML1 channel


Theoretical massNumber of molelcules
Total (without water)262,2944
Polyers262,2944
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)
mammalian endo-lysosomal TRPML1 channel / Mucolipidin / Transient receptor potential-mucolipin 1 / TRPML1


Mass: 65573.617 Da / Num. of mol.: 4
Source: (gene. exp.) Mus musculus / mammal / ハツカネズミ, はつかねずみ /
References: UniProt: Q99J21

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: mammalian endo-lysosomal TRPML1 channel inserting into amphipol
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus
Source (recombinant)Organism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: Amorphous ice
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 2 / Category: RECONSTRUCTION
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 167000 / Symmetry type: POINT

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