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- PDB-9hl8: TRPML1 in complex with compound 8 -

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Basic information

Entry
Database: PDB / ID: 9hl8
TitleTRPML1 in complex with compound 8
ComponentsMucolipin-1
KeywordsMEMBRANE PROTEIN / Ion channel
Function / homology
Function and homology information


positive regulation of lysosome organization / calcium ion export / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / NAADP-sensitive calcium-release channel activity / phagosome maturation / 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 / NAADP-sensitive calcium-release channel activity / phagosome maturation / 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
: / DECANE / DODECANE / Chem-EUJ / HEXANE / N-OCTANE / Mucolipin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsReeks, J. / Mahajan, P. / Clark, M. / Cowan, S.R. / Di Daniel, E. / Earl, C.P. / Fisher, S. / Holvey, R.S. / Jackson, S.M. / Lloyd-Evans, E. ...Reeks, J. / Mahajan, P. / Clark, M. / Cowan, S.R. / Di Daniel, E. / Earl, C.P. / Fisher, S. / Holvey, R.S. / Jackson, S.M. / Lloyd-Evans, E. / Morgillo, C.M. / Mortenson, P.N. / O'Reilly, M. / Richardson, C.J. / Schopf, P. / Tams, D.M. / Waller-Evans, H. / Ward, S.E. / Whibley, S. / Williams, P.A. / Johnson, C.N.
Funding support1items
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, S.R. / Di Daniel, E. / Earl, C.P. / Fisher, S. / Holvey, R.S. / Jackson, S.M. / Lloyd-Evans, E. / Morgillo, C.M. / Mortenson, P.N. / O'Reilly, M. ...Authors: Reeks, J. / Mahajan, P. / Clark, M. / Cowan, S.R. / Di Daniel, E. / Earl, C.P. / Fisher, S. / Holvey, R.S. / Jackson, S.M. / Lloyd-Evans, E. / Morgillo, C.M. / Mortenson, P.N. / O'Reilly, M. / Richardson, C.J. / Schopf, P. / Tams, D.M. / Waller-Evans, H. / Ward, S.E. / Whibley, S. / Williams, P.A. / Johnson, C.N.
History
DepositionDec 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mucolipin-1
B: Mucolipin-1
C: Mucolipin-1
D: Mucolipin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,19444
Polymers282,0744
Non-polymers10,12140
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Mucolipin-1 / ML1 / MG-2 / Mucolipidin / Transient receptor potential channel mucolipin 1 / TRPML1


Mass: 70518.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCOLN1, ML4, TRPML1, MSTP080 / Plasmid: pACEMam2 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9GZU1
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 376 molecules

#3: Chemical
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


Mass: 746.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H49O19P3
#4: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22
#6: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H26
#7: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14
#8: Chemical
ChemComp-A1IV2 / [2,3-bis(chloranyl)phenyl]-[5-methoxy-2-methyl-3-(2-morpholin-4-ylethyl)indol-1-yl]methanone


Mass: 447.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H24Cl2N2O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mucolipin-1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.281 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: Expi293F / Plasmid: pACEMam2
Buffer solutionpH: 7
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
2150 mMSodium chloride1
30.0052 %GDN1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 43.81 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategoryDetails
2EPU3.8image acquisition
4CTFFIND4CTF correctionFor initial estimation
5cryoSPARC4CTF correctionFor CTF refinement
8PHENIX2.8.1model fittingPhaser
10cryoSPARC4initial Euler assignment
11cryoSPARC4final Euler assignment
13cryoSPARC43D reconstruction
14PHENIX1.21rc1-5101model refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113357 / Symmetry type: POINT
Atomic model buildingB value: 54 / Space: REAL
Atomic model buildingDetails: In house structure / Source name: Other / Type: experimental model

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