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- PDB-5w3s: Cryo-electron microscopy structure of a TRPML3 ion channel -

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Database: PDB / ID: 5w3s
TitleCryo-electron microscopy structure of a TRPML3 ion channel
DescriptorMucolipin-3 isoform 1
KeywordsTRANSPORT PROTEIN / transient receptor potential channel / mucolipin / ion channel / membrane transport / TRPML / TRP channel / calcium channel / PIP2 / PI(3 / 5)P2 / lipid-gated channel / mucolipidosis / lysosomal ion channel / lysosome
Specimen sourceCallithrix jacchus / mammal / White-tufted-ear marmoset / コモンマーモセット /
MethodElectron microscopy (2.94 Å resolution / Particle / Single particle)
AuthorsHirschi, M. / Herzik, M.A. / Wie, J. / Suo, Y. / Borschel, W.F. / Ren, D. / Lander, G.C. / Lee, S.Y.
CitationNature, 2017, 550, 411-414

Nature, 2017, 550, 411-414 Yorodumi Papers
Cryo-electron microscopy structure of the lysosomal calcium-permeable channel TRPML3.
Marscha Hirschi / Mark A Herzik / Jinhong Wie / Yang Suo / William F Borschel / Dejian Ren / Gabriel C Lander / Seok-Yong Lee

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 8, 2017 / Release: Oct 11, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 11, 2017Structure modelrepositoryInitial release
1.1Oct 25, 2017Structure modelDatabase referencescitation_citation.pdbx_database_id_PubMed / _citation.title
1.2Nov 1, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Deposited unit
A: Mucolipin-3 isoform 1
B: Mucolipin-3 isoform 1
C: Mucolipin-3 isoform 1
D: Mucolipin-3 isoform 1
hetero molecules

Theoretical massNumber of molelcules
Total (without water)269,34026

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)33250
ΔGint (kcal/M)-356
Surface area (Å2)87220


#1: Polypeptide(L)
Mucolipin-3 isoform 1

Mass: 65092.301 Da / Num. of mol.: 4 / Mutation: N138Q
Source: (gene. exp.) Callithrix jacchus / mammal / コモンマーモセット /
References: UniProt: F6RG56

Cellular component

Molecular function

  • intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity (GO: 0097682)
  • phosphatidylinositol-3,5-bisphosphate binding (GO: 0080025)

Biological process

#2: Chemical

Mass: 486.726 Da / Num. of mol.: 12 / Formula: C31H50O4
#3: Chemical

Mass: 22.990 Da / Num. of mol.: 6 / Formula: Na
#4: Chemical

Mass: 748.065 Da / Num. of mol.: 4 / Formula: C41H82NO8P
#5: WaterChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 4 / Formula: H2O

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Transient Receptor Potential Mucolipin 3 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.26 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Callithrix jacchus
Source (recombinant)Organism: Spodoptera frugiperda / Plasmid: pFastBac / Strain: Sf9
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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 recordingAverage exposure time: 12 sec. / Electron dose: 63 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
SymmetryPoint symmetry: C4
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 104084 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00631924
ELECTRON MICROSCOPYf_angle_d1.37557196
ELECTRON MICROSCOPYf_dihedral_angle_d9.38413092
ELECTRON MICROSCOPYf_chiral_restr0.0502588
ELECTRON MICROSCOPYf_plane_restr0.0044784

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