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- EMDB-48144: ML2-SA1/PI(3,5)P2 bound TRPML2 in an open state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48144
TitleML2-SA1/PI(3,5)P2 bound TRPML2 in an open state
Map dataML2-SA1/PI(3,5)P2 bound TRPML2 in an open state
Sample
  • Complex: ML2-SA1/PI(3,5)P2 bound TRPML2
    • Protein or peptide: Mucolipin-2
  • Ligand: (3aS,4S,7R,7aS)-3-(2,6-dichlorophenyl)-3a,4,5,6,7,7a-hexahydro-4,7-methano-1,2-benzoxazole
  • Ligand: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate
KeywordsTRPML / calcium channel / ion transport / 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: 2.61 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: ML2-SA1/PI(3,5)P2 bound TRPML2 in an open 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_48144.png

Downloads & links

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Map

FileDownload / File: emd_48144.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationML2-SA1/PI(3,5)P2 bound TRPML2 in an open state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.43595678 - 0.9437092
Average (Standard dev.)0.0009285805 (±0.023512287)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_48144_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_48144_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ML2-SA1/PI(3,5)P2 bound TRPML2

EntireName: ML2-SA1/PI(3,5)P2 bound TRPML2
Components
  • Complex: ML2-SA1/PI(3,5)P2 bound TRPML2
    • Protein or peptide: Mucolipin-2
  • Ligand: (3aS,4S,7R,7aS)-3-(2,6-dichlorophenyl)-3a,4,5,6,7,7a-hexahydro-4,7-methano-1,2-benzoxazole
  • Ligand: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate

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Supramolecule #1: ML2-SA1/PI(3,5)P2 bound TRPML2

SupramoleculeName: ML2-SA1/PI(3,5)P2 bound TRPML2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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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Macromolecule #2: (3aS,4S,7R,7aS)-3-(2,6-dichlorophenyl)-3a,4,5,6,7,7a-hexahydro-4,...

MacromoleculeName: (3aS,4S,7R,7aS)-3-(2,6-dichlorophenyl)-3a,4,5,6,7,7a-hexahydro-4,7-methano-1,2-benzoxazole
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1BI6
Molecular weightTheoretical: 282.165 Da

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Macromolecule #3: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bi...

MacromoleculeName: (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate
type: ligand / ID: 3 / Number of copies: 4 / Formula: EUJ
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-EUJ:
(2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate

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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: GATAN K3 BIOQUANTUM (6k 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: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108226
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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