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- EMDB-48139: Apo TRPML2 in a closed state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48139
TitleApo TRPML2 in a closed state
Map data
Sample
  • Complex: Apo TRPML2
    • Protein or peptide: Mucolipin-2
KeywordsTRPML / calcium channel / ion transport / cryo-EM / membrane protein
Function / homology
Function and homology information


positive regulation of macrophage inflammatory protein 1 alpha production / macrophage migration / NAADP-sensitive calcium-release channel activity / positive regulation of chemokine (C-C motif) ligand 5 production / iron ion transmembrane transporter activity / neutrophil migration / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production / TRP channels / calcium ion transmembrane transport ...positive regulation of macrophage inflammatory protein 1 alpha production / macrophage migration / NAADP-sensitive calcium-release channel activity / positive regulation of chemokine (C-C motif) ligand 5 production / iron ion transmembrane transporter activity / neutrophil migration / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production / TRP channels / calcium ion transmembrane transport / calcium channel activity / recycling endosome membrane / late endosome membrane / protein transport / adaptive immune response / lysosome / innate immune response / identical protein binding / membrane / plasma membrane
Similarity search - Function
Mucolipin / : / Mucolipin, extracytosolic domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsSchmiege P / Li X
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149533 United States
CitationJournal: To Be Published
Title: Apo TRPML2 in a closed state
Authors: Schmiege P / Li X
History
DepositionDec 3, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48139.png

Downloads & links

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Map

FileDownload / File: emd_48139.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 320 pix.
= 236.16 Å		0.74 Å/pix.
x 320 pix.
= 236.16 Å		0.74 Å/pix.
x 320 pix.
= 236.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.738 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.062
Minimum - Maximum-0.26283374 - 0.42738813
Average (Standard dev.)0.001553963 (±0.016493438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 236.15999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48139_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48139_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apo TRPML2

EntireName: Apo TRPML2
Components
  • Complex: Apo TRPML2
    • Protein or peptide: Mucolipin-2

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Supramolecule #1: Apo TRPML2

SupramoleculeName: Apo TRPML2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 66.016297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MARQPYRFPQ ARIPERGSGV FRLTVRNAMA HRDSEMKEEC LREDLKFYFM SPCEKYRARR QIPWKLGLQI LKIVMVTTQL VRFGLSNQL VVAFKEDNTV AFKHLFLKGY SGTDEDDYSC SVYTQEDAYE SIFFAINQYH QLKDITLGTL GYGENEDNRI G LKVCKQHY ...String:
MARQPYRFPQ ARIPERGSGV FRLTVRNAMA HRDSEMKEEC LREDLKFYFM SPCEKYRARR QIPWKLGLQI LKIVMVTTQL VRFGLSNQL VVAFKEDNTV AFKHLFLKGY SGTDEDDYSC SVYTQEDAYE SIFFAINQYH QLKDITLGTL GYGENEDNRI G LKVCKQHY KKGTMFPSNE TLNIDNDVEL DCVQLDLQDL SKKPPDWKNS SFFRLEFYRL LQVEISFHLK GIDLQTIHSR EL PDCYVFQ NTIIFDNKAH SGKIKIYFDS DAKIEECKDL NIFGSTQKNA QYVLVFDAFV IVICLASLIL CTRSIVLALR LRK RFLNFF LEKYKRPVCD TDQWEFINGW YVLVIISDLM TIIGSILKME IKAKNLTNYD LCSIFLGTST LLVWVGVIRY LGYF QAYNV LILTMQASLP KVLRFCACAG MIYLGYTFCG WIVLGPYHDK FENLNTVAEC LFSLVNGDDM FATFAQIQQK SILVW LFSR LYLYSFISLF IYMILSLFIA LITDSYDTIK KFQQNGFPET DLQEFLKECS SKEEYQKESS AFLSCICCRR RKRSDD HLI PIS

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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81285
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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