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- EMDB-38930: Cryo-EM reveals cholesterol binding in the lysosomal GPCR-like pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-38930
TitleCryo-EM reveals cholesterol binding in the lysosomal GPCR-like protein LYCHOS
Map data
Sample
  • Complex: Cholesterol-bound LYCHOS
    • Protein or peptide: Lysosomal cholesterol signaling protein
  • Ligand: SODIUM ION
  • Ligand: CHOLESTEROL
  • Ligand: [(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate
  • Ligand: water
Keywordscholesterol / membrane protein / lysosome
Function / homology
Function and homology information


cellular response to cholesterol / cholesterol binding / negative regulation of BMP signaling pathway / positive regulation of TORC1 signaling / cellular response to amino acid starvation / transmembrane transport / cognition / intracellular signal transduction / lysosomal membrane / extracellular exosome
Similarity search - Function
Integral membrane protein GPR155, DEP domain / Membrane transport protein / Membrane transport protein / : / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Lysosomal cholesterol signaling protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsZhao J / Shen QY / Zhang Y / Shao ZH
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Cryo-EM reveals cholesterol binding in the lysosomal GPCR-like protein LYCHOS.
Authors: Jie Zhao / Qingya Shen / Xihao Yong / Xin Li / Xiaowen Tian / Suyue Sun / Zheng Xu / Xiaoyu Zhang / Lu Zhang / Hao Yang / Zhenhua Shao / Haoxing Xu / Yiyang Jiang / Yan Zhang / Wei Yan /
Abstract: Cholesterol plays a pivotal role in modulating the activity of mechanistic target of rapamycin complex 1 (mTOR1), thereby regulating cell growth and metabolic homeostasis. LYCHOS, a lysosome- ...Cholesterol plays a pivotal role in modulating the activity of mechanistic target of rapamycin complex 1 (mTOR1), thereby regulating cell growth and metabolic homeostasis. LYCHOS, a lysosome-localized G-protein-coupled receptor-like protein, emerges as a cholesterol sensor and is capable of transducing the cholesterol signal to affect the mTORC1 function. However, the precise mechanism by which LYCHOS recognizes cholesterol remains unknown. Here, using cryo-electron microscopy, we determined the three-dimensional structural architecture of LYCHOS in complex with cholesterol molecules, revealing a unique arrangement of two sequential structural domains. Through a comprehensive analysis of this structure, we elucidated the specific structural features of these two domains and their collaborative role in the process of cholesterol recognition by LYCHOS.
History
DepositionJan 31, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38930.png

Downloads & links

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Map

FileDownload / File: emd_38930.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0109
Minimum - Maximum-0.07693682 - 0.11524042
Average (Standard dev.)-0.000044671982 (±0.0020475846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38930_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38930_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cholesterol-bound LYCHOS

EntireName: Cholesterol-bound LYCHOS
Components
  • Complex: Cholesterol-bound LYCHOS
    • Protein or peptide: Lysosomal cholesterol signaling protein
  • Ligand: SODIUM ION
  • Ligand: CHOLESTEROL
  • Ligand: [(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate
  • Ligand: water

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Supramolecule #1: Cholesterol-bound LYCHOS

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

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Macromolecule #1: Lysosomal cholesterol signaling protein

MacromoleculeName: Lysosomal cholesterol signaling protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.876375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKPTAVTH GFNSTNDPPS MSITRLFPAL LECFGIVLCG YIAGRANVIT STQAKGLGNF VSRFALPAL LFKNMVVLNF SNVDWSFLYS ILIAKASVFF IVCVLTLLVA SPDSRFSKAG LFPIFATQSN DFALGYPIVE A LYQTTYPE ...String:
MKTIIALSYI FCLVFADYKD DDDKPTAVTH GFNSTNDPPS MSITRLFPAL LECFGIVLCG YIAGRANVIT STQAKGLGNF VSRFALPAL LFKNMVVLNF SNVDWSFLYS ILIAKASVFF IVCVLTLLVA SPDSRFSKAG LFPIFATQSN DFALGYPIVE A LYQTTYPE YLQYIYLVAP ISLMMLNPIG FIFCEIQKWK DTQNASQNKI KIVGLGLLRV LQNPIVFMVF IGIAFNFILD RK VPVYVEN FLDGLGNSFS GSALFYLGLT MVGKIKRLKK SAFVVLILLI TAKLLVLPLL CREMVELLDK GDSVVNHTSL SNY AFLYGV FPVAPGVAIF ATQFNMEVEI ITSGMVISTF VSAPIMYVSA WLLTFPTMDP KPLAYAIQNV SFDISIVSLI SLIW SLAIL LLSKKYKQLP HMLTTNLLIA QSIVCAGMMI WNFVKEKNFV GQILVFVLLY SSLYSTYLWT GLLAISLFLL KKRER VQIP VGIIIISGWG IPALLVGVLL ITGKHNGDSI DSAFFYGKEQ MITTAVTLFC SILIAGISLM CMNQTAQAGS YEGFDQ SQS HKVVEPGNTA FEESPAPVNE PELFTSSIPE TSCCSCSMGN GELHCPSIEP IANTSTSEPV IPSFEKNNHC VSRCNSQ SC ILAQEEEQYL QSGDQQLTRH VLLCLLLIIG LFANLSSCLW WLFNQEPGRL YVELQFFCAV FNFGQGFISF GIFGLDKH L IILPFKRRLE FLWNNKDTAE NRDSPVSEEI KMTCQQFIHY HRDLCIRNIV KERRCGAKTS AGTFCGCDLV SWLIEVGLA SDRGEAVIYG DRLVQGGVIQ HITNEYEFRD EYLFYRFLQK

UniProtKB: Lysosomal cholesterol signaling protein

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 5 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #4: [(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy...

MacromoleculeName: [(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate
type: ligand / ID: 4 / Number of copies: 1 / Formula: DKB
Molecular weightTheoretical: 720.012 Da
Chemical component information

ChemComp-DKB:
[(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104127
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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