[English] 日本語
Yorodumi
- EMDB-48135: ML2-SA1 bound TRPML1-V432A/A433G in a partially open state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48135
TitleML2-SA1 bound TRPML1-V432A/A433G in a partially open state
Map data
Sample
  • Complex: ML2-SA1 bound TRPML1-V432A/A433G
    • Protein or peptide: Mucolipin-1
  • Ligand: (3aS,4S,7R,7aS)-3-(2,6-dichlorophenyl)-3a,4,5,6,7,7a-hexahydro-4,7-methano-1,2-benzoxazole
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: 2.42 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: ML2-SA1 bound TRPML1-V432A/A433G in a partially 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

-
Structure visualization

Supplemental images

emd_48135.png

Downloads & links

-
Map

FileDownload / File: emd_48135.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 265.68 Å		0.74 Å/pix.
x 360 pix.
= 265.68 Å		0.74 Å/pix.
x 360 pix.
= 265.68 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: 0.084
Minimum - Maximum-0.37661117 - 0.653249
Average (Standard dev.)0.0005375072 (±0.019977948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 265.68 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_48135_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_48135_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ML2-SA1 bound TRPML1-V432A/A433G

EntireName: ML2-SA1 bound TRPML1-V432A/A433G
Components
  • Complex: ML2-SA1 bound TRPML1-V432A/A433G
    • Protein or peptide: Mucolipin-1
  • Ligand: (3aS,4S,7R,7aS)-3-(2,6-dichlorophenyl)-3a,4,5,6,7,7a-hexahydro-4,7-methano-1,2-benzoxazole

-
Supramolecule #1: ML2-SA1 bound TRPML1-V432A/A433G

SupramoleculeName: ML2-SA1 bound TRPML1-V432A/A433G / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
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: 66.039883 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKT APAGPRGSET ERLLTPNPGY GTQAGPSPAP PTPPEEEDLR RRLKYFFMSP CDKFRAKGRK PCKLMLQVVK ILVVTVQLI LFGLSNQLAV TFREENTIAF RHLFLLGYSD GADDTFAAYT REQLYQAIFH AVDQYLALPD VSLGRYAYVR G GGDPWTNG ...String:
MDYKDDDDKT APAGPRGSET ERLLTPNPGY GTQAGPSPAP PTPPEEEDLR RRLKYFFMSP CDKFRAKGRK PCKLMLQVVK ILVVTVQLI LFGLSNQLAV TFREENTIAF RHLFLLGYSD GADDTFAAYT REQLYQAIFH AVDQYLALPD VSLGRYAYVR G GGDPWTNG SGLALCQRYY HRGHVDPAND TFDIDPMVVT DCIQVDPPER PPPPPSDDLT LLESSSSYKN LTLKFHKLVN VT IHFRLKT INLQSLINNE IPDCYTFSVL ITFDNKAHSG RIPISLETQA HIQECKHPSV FQHGDNSFRL LFDVVVILTC SLS FLLCAR SLLRGFLLQN EFVGFMWRQR GRVISLWERL EFVNGWYILL VTSDVLTISG TIMKIGIEAK NLASYDVCSI LLGT STLLV WVGVIRYLTF FHNYNILIAT LRVALPSVMR FCCCAGVIYL GYCFCGWIVL GPYHVKFRSL SMVSECLFSL INGDD MFVT FAAMQAQQGR SSLVWLFSQL YLYSFISLFI YMVLSLFIAL ITGAYDTIKH PGGAGAEESE LQAYIAQCQD SPTSGK FRR GSGSACSLLC CCGRDPSEEH SLLVN

UniProtKB: Mucolipin-1

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 200542
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more