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- EMDB-30924: CryoEM structure of full length mouse TRPML2 -

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Basic information

Entry
Database: EMDB / ID: EMD-30924
TitleCryoEM structure of full length mouse TRPML2
Map data
Sample
  • Organelle or cellular component: TRPML2
    • Protein or peptide: Mucolipin-2
Keywordstransient receptor potential mucolipin channels / TRP channel / TRPML2 / MEMBRANE PROTEIN
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 / iron ion transmembrane transporter 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 ...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 / iron ion transmembrane transporter 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 / lysosome / innate immune response / identical protein binding / membrane
Similarity search - Function
Mucolipin / : / Mucolipin, extracytosolic domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsSong XJ / Li J / Duan JJ / Zhang J
Funding support1 items
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, 2021-
Header (metadata) releaseMar 23, 2022-
Map releaseMar 23, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_30924.png

Downloads & links

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Map

FileDownload / File: emd_30924.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-1.0711873 - 2.7208974
Average (Standard dev.)0.0024367862 (±0.07108339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : TRPML2

EntireName: TRPML2
Components
  • Organelle or cellular component: TRPML2
    • Protein or peptide: Mucolipin-2

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Supramolecule #1: TRPML2

SupramoleculeName: TRPML2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Mucolipin-2

MacromoleculeName: Mucolipin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 60.010258 KDa
Recombinant expressionOrganism: Mammalian expression vector HA-MCS-pcDNA3.1 (others)
SequenceString: MPGDEETLDL PAWNRVPDLT WGPHHRSAMA SLDSEVREEC LREDLKFYFM SPCEKYRARR QIPWKLGLQI LKIVMVTTQL VRFGLSNQL VVAFKEDNTV AFKHLFLKGF SGVDEDDYSC SIYTQENTYE SIFFAIKQYR HLKNISLATL GYGESEDNRT G LKVCKQHY ...String:
MPGDEETLDL PAWNRVPDLT WGPHHRSAMA SLDSEVREEC LREDLKFYFM SPCEKYRARR QIPWKLGLQI LKIVMVTTQL VRFGLSNQL VVAFKEDNTV AFKHLFLKGF SGVDEDDYSC SIYTQENTYE SIFFAIKQYR HLKNISLATL GYGESEDNRT G LKVCKQHY KTGAMFSSNE TLNIDSDIET DCIHLDLQVL TTEPEDWAQT SFFRLDFYRL VQVDISFALK GIDLQAVHSR EI PDCYLFQ NTITFDNTAH SGKIKIYLNS EANIEECKNM NISGSTQRST HYLLVFDVFV IMICLASLIL CTRSIVLALR LRK RFLNFF LEKYKQRVCG ADQWEFVNGW YVLVTISDLM TIIGSILKME IKAKKLTNYD VCSILLGTST LFVWVGVIRY LGYF QTYNV LILTMQASLP KVLRFCACAG MIYLGYTFCG WIVLGPYHEK FENLNIVAEC LFSLVNGDDM FATFAQIQQK SILVW LFSR LYLYSFISLF IYMVLSLFIA LITDSYHTIK KYQQ

UniProtKB: Mucolipin-2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21734
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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