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- PDB-7dys: CryoEM structure of full length mouse TRPML2 -

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Basic information

Entry
Database: PDB / ID: 7dys
TitleCryoEM structure of full length mouse TRPML2
ComponentsMucolipin-2
KeywordsMEMBRANE PROTEIN / transient receptor potential mucolipin channels / TRP channel / TRPML2
Function / homology
Function and homology information


regulation of chemokine (C-X-C motif) ligand 2 production / macrophage migration / positive regulation of macrophage inflammatory protein 1 alpha production / NAADP-sensitive calcium-release channel activity / positive regulation of chemokine (C-C motif) ligand 5 production / neutrophil migration / TRP channels / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of chemokine production ...regulation of chemokine (C-X-C motif) ligand 2 production / macrophage migration / positive regulation of macrophage inflammatory protein 1 alpha production / NAADP-sensitive calcium-release channel activity / positive regulation of chemokine (C-C motif) ligand 5 production / neutrophil migration / TRP channels / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of chemokine production / recycling endosome / recycling endosome membrane / protein transport / adaptive immune response / membrane => GO:0016020 / lysosome / innate immune response / identical protein binding / membrane
Similarity search - Function
Mucolipin / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsSong, X.J. / Li, J. / Duan, J.J. / Zhang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Biol Chem / Year: 2022
Title: Cryo-EM structure of mouse TRPML2 in lipid nanodiscs.
Authors: Xiaojing Song / Jian Li / Miao Tian / Huaiyi Zhu / Xiaohui Hu / Yuting Zhang / Yanru Cao / Heyang Ye / Peter J McCormick / Bo Zeng / Yang Fu / Jingjing Duan / Jin Zhang /
Abstract: In mammalians, transient receptor potential mucolipin ion channels (TRPMLs) exhibit variable permeability to cations such as Ca, Fe, Zn, and Na and can be activated by the phosphoinositide PI(3,5)P2 ...In mammalians, transient receptor potential mucolipin ion channels (TRPMLs) exhibit variable permeability to cations such as Ca, Fe, Zn, and Na and can be activated by the phosphoinositide PI(3,5)P2 in the endolysosomal system. Loss or dysfunction of TRPMLs has been implicated in lysosomal storage disorders, infectious diseases, and metabolic diseases. TRPML2 has recently been identified as a mechanosensitive and hypotonicity-sensitive channel in endolysosomal organelles, which distinguishes it from TRPML1 and TRPML3. However, the molecular and gating mechanism of TRPML2 remains elusive. Here, we present the cryo-EM structure of the full-length mouse TRPML2 in lipid nanodiscs at 3.14 Å resolution. The TRPML2 homotetramer structure at pH 7.4 in the apo state reveals an inactive conformation and some unique features of the extracytosolic/luminal domain and voltage sensor-like domain that have implications for the ion-conducting pathway. This structure enables new comparisons between the different subgroups of TRPML channels with available structures and provides structural insights into the conservation and diversity of TRPML channels. These comparisons have broad implications for understanding a variety of molecular mechanisms of TRPMLs in different pH conditions, including with and without bound agonists and antagonists.
History
DepositionJan 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mucolipin-2
B: Mucolipin-2
C: Mucolipin-2
D: Mucolipin-2


Theoretical massNumber of molelcules
Total (without water)240,0414
Polymers240,0414
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Mucolipin-2 / Transient receptor potential channel mucolipin 2 / TRPML2


Mass: 60010.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mcoln2
Production host: Mammalian expression vector HA-MCS-pcDNA3.1 (others)
References: UniProt: Q8K595

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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: TRPML2 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Mammalian expression vector HA-MCS-pcDNA3.1 (others)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21734 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00712301
ELECTRON MICROSCOPYf_angle_d0.89216694
ELECTRON MICROSCOPYf_dihedral_angle_d4.6567136
ELECTRON MICROSCOPYf_chiral_restr0.0542014
ELECTRON MICROSCOPYf_plane_restr0.0062027

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