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- EMDB-31753: Cryo-EM structure of Patched in lipid nanodisc - the wildtype, 3.... -

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Basic information

Entry
Database: EMDB / ID: EMD-31753
TitleCryo-EM structure of Patched in lipid nanodisc - the wildtype, 3.5 angstrom (re-processed with dataset of 7dzq)
Map data
Sample
  • Complex: Ptc1 in lipid nanodisc
    • Protein or peptide: Protein patched homolog 1,Protein patched homolog 1
  • Ligand: CHOLESTEROL
  • Ligand: (2S)-2-azanyl-3-[[(2S)-3-butanoyloxy-2-dec-9-enoyloxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCaveolae / Hedgehog signaling / Lipid nanodisc / Patched / Ptc1 dimer / membrane protein
Function / homology
Function and homology information


cell differentiation involved in kidney development / response to chlorate / cell proliferation involved in metanephros development / hindlimb morphogenesis / Ligand-receptor interactions / Activation of SMO / epidermal cell fate specification / neural plate axis specification / neural tube patterning / hedgehog receptor activity ...cell differentiation involved in kidney development / response to chlorate / cell proliferation involved in metanephros development / hindlimb morphogenesis / Ligand-receptor interactions / Activation of SMO / epidermal cell fate specification / neural plate axis specification / neural tube patterning / hedgehog receptor activity / smoothened binding / spinal cord motor neuron differentiation / hedgehog family protein binding / neural tube formation / negative regulation of multicellular organism growth / limb morphogenesis / Hedgehog 'on' state / mammary gland duct morphogenesis / mammary gland epithelial cell differentiation / pharyngeal system development / prostate gland development / somite development / negative regulation of cell division / Hedgehog 'off' state / patched binding / smooth muscle tissue development / pattern specification process / cell fate determination / cellular response to cholesterol / mammary gland development / embryonic limb morphogenesis / dorsal/ventral pattern formation / commissural neuron axon guidance / metanephric collecting duct development / response to alkaloid / branching involved in ureteric bud morphogenesis / regulation of growth / dorsal/ventral neural tube patterning / spermatid development / positive regulation of epidermal cell differentiation / cholesterol binding / epidermis development / keratinocyte proliferation / dendritic growth cone / embryonic organ development / heart morphogenesis / positive regulation of cholesterol efflux / response to mechanical stimulus / response to retinoic acid / negative regulation of osteoblast differentiation / neural tube closure / axonal growth cone / animal organ morphogenesis / liver regeneration / regulation of mitotic cell cycle / cyclin binding / protein localization to plasma membrane / negative regulation of smoothened signaling pathway / brain development / protein processing / negative regulation of epithelial cell proliferation / caveola / in utero embryonic development / apical part of cell / glucose homeostasis / response to estradiol / regulation of protein localization / regulation of cell population proliferation / heparin binding / midbody / cilium / postsynaptic membrane / response to xenobiotic stimulus / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular region / zinc ion binding / plasma membrane
Similarity search - Function
Transformer protein 2 N-terminal domain / Transmembrane receptor, patched / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
Similarity search - Domain/homology
Protein patched homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLuo Y / Zhao Y
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570748 China
National Natural Science Foundation of China (NSFC)U1632127 China
Chinese Academy of SciencesXDB37020204 China
Chinese Academy of SciencesQYZDB-SSW-SMC037 China
CitationJournal: Structure / Year: 2021
Title: Cryo-EM study of patched in lipid nanodisc suggests a structural basis for its clustering in caveolae.
Authors: Yitian Luo / Guoyue Wan / Xiang Zhang / Xuan Zhou / Qiuwen Wang / Jialin Fan / Hongmin Cai / Liya Ma / Hailong Wu / Qianhui Qu / Yao Cong / Yun Zhao / Dianfan Li /
Abstract: The 12-transmembrane protein Patched (Ptc1) acts as a suppressor for Hedgehog (Hh) signaling by depleting sterols in the cytoplasmic membrane leaflet that are required for the activation of ...The 12-transmembrane protein Patched (Ptc1) acts as a suppressor for Hedgehog (Hh) signaling by depleting sterols in the cytoplasmic membrane leaflet that are required for the activation of downstream regulators. The positive modulator Hh inhibits Ptc1's transporter function by binding to Ptc1 and its co-receptors, which are locally concentrated in invaginated microdomains known as caveolae. Here, we reconstitute the mouse Ptc1 into lipid nanodiscs and determine its structure using single-particle cryoelectron microscopy. The structure is overall similar to those in amphipol and detergents but displays various conformational differences in the transmembrane region. Although most particles show monomers, we observe Ptc1 dimers with distinct interaction patterns and different membrane curvatures, some of which are reminiscent of caveolae. We find that an extramembranous "hand-shake" region rich in hydrophobic and aromatic residues mediates inter-Ptc1 interactions under different membrane curvatures. Our data provide a plausible framework for Ptc1 clustering in the highly curved caveolae.
History
DepositionAug 20, 2021-
SupersessionSep 22, 2021ID: EMD-30928
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.355
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.355
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7v6y
  • Surface level: 0.355
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7v6y
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31753.png

Downloads & links

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Map

FileDownload / File: emd_31753.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 264 pix.
= 216.48 Å		0.82 Å/pix.
x 264 pix.
= 216.48 Å		0.82 Å/pix.
x 264 pix.
= 216.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.355 / Movie #1: 0.355
Minimum - Maximum-2.5728045 - 4.252389
Average (Standard dev.)0.001684434 (±0.074830465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 216.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z216.480216.480216.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-140-140-140
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-2.5734.2520.002

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Supplemental data

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Sample components

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Entire : Ptc1 in lipid nanodisc

EntireName: Ptc1 in lipid nanodisc
Components
  • Complex: Ptc1 in lipid nanodisc
    • Protein or peptide: Protein patched homolog 1,Protein patched homolog 1
  • Ligand: CHOLESTEROL
  • Ligand: (2S)-2-azanyl-3-[[(2S)-3-butanoyloxy-2-dec-9-enoyloxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ptc1 in lipid nanodisc

SupramoleculeName: Ptc1 in lipid nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 160 kDa/nm

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Macromolecule #1: Protein patched homolog 1,Protein patched homolog 1

MacromoleculeName: Protein patched homolog 1,Protein patched homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 121.637617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSASAGNAA GALGRQAGGG RRRRTGGPHR AAPDRDYLHR PSYCDAAFAL EQISKGKATG RKAPLWLRAK FQRLLFKLGC YIQKNCGKF LVVGLLIFGA FAVGLKAANL ETNVEELWVE VGGRVSRELN YTRQKIGEEA MFNPQLMIQT PKEEGANVLT T EALLQHLD ...String:
MGSASAGNAA GALGRQAGGG RRRRTGGPHR AAPDRDYLHR PSYCDAAFAL EQISKGKATG RKAPLWLRAK FQRLLFKLGC YIQKNCGKF LVVGLLIFGA FAVGLKAANL ETNVEELWVE VGGRVSRELN YTRQKIGEEA MFNPQLMIQT PKEEGANVLT T EALLQHLD SALQASRVHV YMYNRQWKLE HLCYKSGELI TETGYMDQII EYLYPCLIIT PLDCFWEGAK LQSGTAYLLG KP PLRWTNF DPLEFLEELK KINYQVDSWE EMLNKAEVGH GYMDRPCLNP ADPDCPATAP NKNSTKPLDV ALVLNGGCQG LSR KYMHWQ EELIVGGTVK NATGKLVSAH ALQTMFQLMT PKQMYEHFRG YDYVSHINWN EDRAAAILEA WQRTYVEVVH QSVA PNSTQ KVLPFTTTTL DDILKSFSDV SVIRVASGYL LMLAYACLTM LRWDCSKSQG AVGLAGVLLV ALSVAAGLGL CSLIG ISFN AATTQVLPFL ALGVGVDDVF LLAHAFSETG QNKRIPFEDR TGECLKRTGA SVALTSISNV TAFFMAALIP IPALRA FSL QAAVVVVFNF AMVLLIFPAI LSMDLYRRED RRLDIFCCFT SPCVSRVIQV EPQEPPCTKW TLSSFAEKHY APFLLKP KA KVVVILLFLG LLGVSLYGTT RVRDGLDLTD IVPRETREYD FIAAQFKYFS FYNMYIVTQK ADYPNIQHLL YDLHKSFS N VKYVMLEENK QLPQMWLHYF RDWLQGLQDA FDSDWETGRI MPNNYKNGSD DGVLAYKLLV QTGSRDKPID ISQLTKQRL VDADGIINPS AFYIYLTAWV SNDPVAYAAS QANIRPHRPE WVHDKADYMP ETRLRIPAAE PIEYAQFPFY LNGLRDTSDF VEAIEKVRV ICNNYTSLGL SSYPNGYPFL FWEQYISLRH WLLLSISVVL ACTFLVCAVF LLNPWTAGII VMVLALMTVE L FGMMGLIG IKLSAVPVVI LIASVGIGVE FTVHVALAFL TAIGDKNHRA MLALEHMFAP VLDGAVSTLL GVLMLAGSEF DF IVRYFFA VLAILTVLGV LNGLVLLPVL LSFFGPCPEV SPANGTLEVL FQG

UniProtKB: Protein patched homolog 1, Protein patched homolog 1

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #4: (2S)-2-azanyl-3-[[(2S)-3-butanoyloxy-2-dec-9-enoyloxy-propoxy]-ox...

MacromoleculeName: (2S)-2-azanyl-3-[[(2S)-3-butanoyloxy-2-dec-9-enoyloxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid
type: ligand / ID: 4 / Number of copies: 1 / Formula: 5VI
Molecular weightTheoretical: 481.474 Da
Chemical component information

ChemComp-5VI:
(2S)-2-azanyl-3-[[(2S)-3-butanoyloxy-2-dec-9-enoyloxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration8.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMHEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
0.5 mMCaCl2calsium chloride
0.1 mMEDTAEthylenediaminetetraacetic acid
0.2 mMTCEPtris(2-carboxyethyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Average exposure time: 2.23 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.1 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.5 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

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Image processing

Particle selectionNumber selected: 1363356
Startup modelType of model: NONE
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 172299
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 1
Software - Name: cryoSPARC (ver. 3.2)
Final 3D classificationNumber classes: 2 / Avg.num./class: 174964 / Software - Name: cryoSPARC (ver. 3.2)

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Atomic model buiding 1

Initial modelPDB ID:

6mg8


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 57.04
Output model

PDB-7v6y:
Cryo-EM structure of Patched in lipid nanodisc - the wildtype, 3.5 angstrom (re-processed with dataset of 7dzq)

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