[English] 日本語
Yorodumi
- EMDB-52249: TRPML1 in complex with compound 10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52249
TitleTRPML1 in complex with compound 10
Map dataCryoSPARC sharpened masked filtered map
Sample
  • Complex: Mucolipin-1
    • Protein or peptide: Mucolipin-1
  • Ligand: HEXANE
  • Ligand: DODECANE
  • Ligand: N-OCTANE
  • 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
  • Ligand: HEXADECANE
  • Ligand: DECANE
  • Ligand: N-[2-[4-(2-methoxyphenyl)piperazin-1-yl]phenyl]benzenesulfonamide
  • Ligand: water
KeywordsIon channel / MEMBRANE 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 / iron ion transmembrane transporter activity / ligand-gated calcium channel activity / cellular response to pH / 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 / iron ion transmembrane transporter activity / ligand-gated calcium channel activity / cellular response to pH / Transferrin endocytosis and recycling / iron ion transmembrane transport / 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 / transferrin transport / 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: 2.1 Å
AuthorsReeks J / Mahajan P / Clark M / Cowan SR / Di Daniel E / Earl CP / Fisher S / Holvey RS / Jackson SM / Lloyd-Evans E ...Reeks J / Mahajan P / Clark M / Cowan SR / Di Daniel E / Earl CP / Fisher S / Holvey RS / Jackson SM / Lloyd-Evans E / Morgillo CM / Mortenson PN / O'Reilly M / Richardson CJ / Schopf P / Tams DM / Waller-Evans H / Ward SE / Whibley S / Williams PA / Johnson CN
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Enabling High Throughput Electron Cryo-microscopy for Structure-based Design
Authors: Reeks J / Mahajan P / Clark M / Cowan SR / Di Daniel E / Earl CP / Fisher S / Holvey RS / Jackson SM / Lloyd-Evans E / Morgillo CM / Mortenson PN / O'Reilly M / Richardson CJ / Schopf P / ...Authors: Reeks J / Mahajan P / Clark M / Cowan SR / Di Daniel E / Earl CP / Fisher S / Holvey RS / Jackson SM / Lloyd-Evans E / Morgillo CM / Mortenson PN / O'Reilly M / Richardson CJ / Schopf P / Tams DM / Waller-Evans H / Ward SE / Whibley S / Williams PA / Johnson CN
History
DepositionDec 4, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52249.png

Downloads & links

-
Map

FileDownload / File: emd_52249.map.gz / Format: CCP4 / Size: 783.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoSPARC sharpened masked filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 590 pix.
= 379.429 Å		0.64 Å/pix.
x 590 pix.
= 379.429 Å		0.64 Å/pix.
x 590 pix.
= 379.429 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6431 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.471
Minimum - Maximum-1.6300455 - 3.1949878
Average (Standard dev.)0.0020435404 (±0.041963156)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions590590590
Spacing590590590
CellA=B=C: 379.42902 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_52249_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: CryoSPARC sharpened unmasked unfiltered map

Fileemd_52249_additional_1.map
AnnotationCryoSPARC sharpened unmasked unfiltered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: CryoSPARC sharpened masked filtered map rescaled to 0.5 A/pix

Fileemd_52249_additional_2.map
AnnotationCryoSPARC sharpened masked filtered map rescaled to 0.5 A/pix
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: CryoSPARC non-uniform refinement half map 1

Fileemd_52249_half_map_1.map
AnnotationCryoSPARC non-uniform refinement half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: CryoSPARC non-uniform refinement half map 2

Fileemd_52249_half_map_2.map
AnnotationCryoSPARC non-uniform refinement half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Mucolipin-1

EntireName: Mucolipin-1
Components
  • Complex: Mucolipin-1
    • Protein or peptide: Mucolipin-1
  • Ligand: HEXANE
  • Ligand: DODECANE
  • Ligand: N-OCTANE
  • 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
  • Ligand: HEXADECANE
  • Ligand: DECANE
  • Ligand: N-[2-[4-(2-methoxyphenyl)piperazin-1-yl]phenyl]benzenesulfonamide
  • Ligand: water

+
Supramolecule #1: Mucolipin-1

SupramoleculeName: Mucolipin-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 281 KDa

+
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: 70.518469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHG GSDYKDHDGD YKDHDIDYKD DDDKGGSGGS ENLYFQGPGT APAGPRGSET ERLLTPNPGY GTQAGPSPAP PTPPEEEDL RRRLKYFFMS PCDKFRAKGR KPCKLMLQVV KILVVTVQLI LFGLSNQLAV TFREENTIAF RHLFLLGYSD G ADDTFAAY ...String:
MHHHHHHHHG GSDYKDHDGD YKDHDIDYKD DDDKGGSGGS ENLYFQGPGT APAGPRGSET ERLLTPNPGY GTQAGPSPAP PTPPEEEDL RRRLKYFFMS PCDKFRAKGR KPCKLMLQVV KILVVTVQLI LFGLSNQLAV TFREENTIAF RHLFLLGYSD G ADDTFAAY TREQLYQAIF HAVDQYLALP DVSLGRYAYV RGGGDPWTNG SGLALCQRYY HRGHVDPAND TFDIDPMVVT DC IQVDPPE RPPPPPSDDL TLLESSSSYK NLTLKFHKLV NVTIHFRLKT INLQSLINNE IPDCYTFSVL ITFDNKAHSG RIP ISLETQ AHIQECKHPS VFQHGDNSFR LLFDVVVILT CSLSFLLCAR SLLRGFLLQN EFVGFMWRQR GRVISLWERL EFVN GWYIL LVTSDVLTIS GTIMKIGIEA KNLASYDVCS ILLGTSTLLV WVGVIRYLTF FHNYNILIAT LRVALPSVMR FCCCV AVIY LGYCFCGWIV LGPYHVKFRS LSMVSECLFS LINGDDMFVT FAAMQAQQGR SSLVWLFSQL YLYSFISLFI YMVLSL FIA LITGAYDTIK HPGGAGAEES ELQAYIAQCQ DSPTSGKFRR GSGSACSLLC CCGRDPSEEH SLLVN

UniProtKB: Mucolipin-1

+
Macromolecule #3: HEXANE

MacromoleculeName: HEXANE / type: ligand / ID: 3 / Number of copies: 8 / Formula: HEX
Molecular weightTheoretical: 86.175 Da
Chemical component information

ChemComp-HEX:
HEXANE

+
Macromolecule #4: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 4 / Number of copies: 12 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

+
Macromolecule #5: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 5 / Number of copies: 8 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

+
Macromolecule #6: (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: 6 / 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

+
Macromolecule #7: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 7 / Number of copies: 4 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

+
Macromolecule #8: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 8 / Number of copies: 4 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

+
Macromolecule #9: N-[2-[4-(2-methoxyphenyl)piperazin-1-yl]phenyl]benzenesulfonamide

MacromoleculeName: N-[2-[4-(2-methoxyphenyl)piperazin-1-yl]phenyl]benzenesulfonamide
type: ligand / ID: 9 / Number of copies: 4 / Formula: A1IV4
Molecular weightTheoretical: 423.528 Da

+
Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 296 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7
Component:
ConcentrationName
20.0 mMHEPES
150.0 mMSodium chloride
0.0052 %GDN
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Average electron dose: 39.08 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4)For initial estimation
cryoSPARC (ver. 4)For CTF refinement

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 398353
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: In house structure
RefinementSpace: REAL / Overall B value: 62
Output model

PDB-9hlb:
TRPML1 in complex with compound 10

+
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