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- EMDB-48138: ML-SA5 bound TRPML1 in an open state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48138
TitleML-SA5 bound TRPML1 in an open state
Map data
Sample
  • Complex: ML-SA5 bound TRPML1
    • Protein or peptide: Mucolipin-1
  • Ligand: N4-(3-chloranyl-2-piperidin-1-yl-phenyl)-N1,N1-dimethyl-benzene-1,4-disulfonamide
KeywordsTRPML / calcium channel / ion transport / cryo-EM / TRANSPORT PROTEIN
Function / homology
Function and homology information


positive regulation of lysosome organization / calcium ion export / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / phagosome maturation / NAADP-sensitive calcium-release channel activity / transferrin transport / iron ion transmembrane transporter activity / ligand-gated calcium channel activity / Transferrin endocytosis and recycling / iron ion transmembrane transport ...positive regulation of lysosome organization / calcium ion export / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / phagosome maturation / NAADP-sensitive calcium-release channel activity / transferrin transport / iron ion transmembrane transporter activity / ligand-gated calcium channel activity / Transferrin endocytosis and recycling / iron ion transmembrane transport / cellular response to pH / monoatomic anion channel activity / TRP channels / sodium channel activity / monoatomic cation transport / autophagosome maturation / potassium channel activity / phagocytic cup / monoatomic cation channel activity / release of sequestered calcium ion into cytosol / cellular response to calcium ion / cell projection / calcium ion transmembrane transport / calcium channel activity / phagocytic vesicle membrane / late endosome membrane / late endosome / protein homotetramerization / adaptive immune response / lysosome / receptor complex / endosome membrane / lysosomal membrane / intracellular membrane-bounded organelle / lipid binding / Golgi apparatus / nucleoplasm / 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: 2.75 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)R35 GM149533 United States
CitationJournal: To Be Published
Title: ML-SA5 bound TRPML1 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_48138.png

Downloads & links

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Map

FileDownload / File: emd_48138.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: 0.063
Minimum - Maximum-0.24216177 - 0.47662503
Average (Standard dev.)0.0015292779 (±0.017431883)
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_48138_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_48138_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 : ML-SA5 bound TRPML1

EntireName: ML-SA5 bound TRPML1
Components
  • Complex: ML-SA5 bound TRPML1
    • Protein or peptide: Mucolipin-1
  • Ligand: N4-(3-chloranyl-2-piperidin-1-yl-phenyl)-N1,N1-dimethyl-benzene-1,4-disulfonamide

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Supramolecule #1: ML-SA5 bound TRPML1

SupramoleculeName: ML-SA5 bound TRPML1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mucolipin-1

MacromoleculeName: Mucolipin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.084996 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTAPAGPRGS ETERLLTPNP GYGTQAGPSP APPTPPEEED LRRRLKYFFM SPCDKFRAKG RKPCKLMLQV VKILVVTVQL ILFGLSNQL AVTFREENTI AFRHLFLLGY SDGADDTFAA YTREQLYQAI FHAVDQYLAL PDVSLGRYAY VRGGGDPWTN G SGLALCQR ...String:
MTAPAGPRGS ETERLLTPNP GYGTQAGPSP APPTPPEEED LRRRLKYFFM SPCDKFRAKG RKPCKLMLQV VKILVVTVQL ILFGLSNQL AVTFREENTI AFRHLFLLGY SDGADDTFAA YTREQLYQAI FHAVDQYLAL PDVSLGRYAY VRGGGDPWTN G SGLALCQR YYHRGHVDPA NDTFDIDPMV VTDCIQVDPP ERPPPPPSDD LTLLESSSSY KNLTLKFHKL VNVTIHFRLK TI NLQSLIN NEIPDCYTFS VLITFDNKAH SGRIPISLET QAHIQECKHP SVFQHGDNSF RLLFDVVVIL TCSLSFLLCA RSL LRGFLL QNEFVGFMWR QRGRVISLWE RLEFVNGWYI LLVTSDVLTI SGTIMKIGIE AKNLASYDVC SILLGTSTLL VWVG VIRYL TFFHNYNILI ATLRVALPSV MRFCCCVAVI YLGYCFCGWI VLGPYHVKFR SLSMVSECLF SLINGDDMFV TFAAM QAQQ GRSSLVWLFS QLYLYSFISL FIYMVLSLFI ALITGAYDTI KHPGGAGAEE SELQAYIAQC QDSPTSGKFR RGSGSA CSL LCCCGRDPSE EHSLLVN

UniProtKB: Mucolipin-1

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Macromolecule #2: N4-(3-chloranyl-2-piperidin-1-yl-phenyl)-N1,N1-dimethyl-benzene-1...

MacromoleculeName: N4-(3-chloranyl-2-piperidin-1-yl-phenyl)-N1,N1-dimethyl-benzene-1,4-disulfonamide
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1IVC
Molecular weightTheoretical: 457.995 Da

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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: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99210
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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