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- PDB-6dmo: Cryo-EM structure of human Ptch1 with three mutations L282Q/T500F... -

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Entry
Database: PDB / ID: 6dmo
TitleCryo-EM structure of human Ptch1 with three mutations L282Q/T500F/P504L
ComponentsProtein patched homolog 1
KeywordsPROTEIN BINDING / Receptor / RND family
Function / homologyClass B/2 (Secretin family receptors) / Sterol-sensing domain (SSD) profile. / Patched family / Transmembrane receptor, patched / Protein patched/dispatched / Activation of SMO / Hedgehog 'on' state / Sterol-sensing domain / Hedgehog 'off' state / Ligand-receptor interactions ...Class B/2 (Secretin family receptors) / Sterol-sensing domain (SSD) profile. / Patched family / Transmembrane receptor, patched / Protein patched/dispatched / Activation of SMO / Hedgehog 'on' state / Sterol-sensing domain / Hedgehog 'off' state / Ligand-receptor interactions / hedgehog receptor activity / neural plate axis specification / response to chlorate / cell proliferation involved in metanephros development / cell differentiation involved in kidney development / smoothened signaling pathway involved in dorsal/ventral neural tube patterning / neural tube patterning / smoothened binding / epidermal cell fate specification / hedgehog family protein binding / hindlimb morphogenesis / spinal cord motor neuron differentiation / mammary gland duct morphogenesis / patched binding / somite development / limb morphogenesis / negative regulation of multicellular organism growth / cellular response to cholesterol / negative regulation of smoothened signaling pathway / negative regulation of cell division / positive regulation of cholesterol efflux / renal system development / keratinocyte proliferation / dorsal/ventral pattern formation / pharyngeal system development / positive regulation of epidermal cell differentiation / mammary gland epithelial cell differentiation / cell fate determination / commissural neuron axon guidance / ciliary membrane / smoothened signaling pathway / prostate gland development / regulation of smoothened signaling pathway / embryonic limb morphogenesis / cholesterol binding / embryonic organ development / branching involved in ureteric bud morphogenesis / negative regulation of osteoblast differentiation / negative regulation of epithelial cell proliferation / heart morphogenesis / dendritic growth cone / axonal growth cone / protein localization to plasma membrane / regulation of mitotic cell cycle / protein processing / cyclin binding / response to retinoic acid / animal organ morphogenesis / regulation of protein localization / neural tube closure / liver regeneration / response to mechanical stimulus / endocytic vesicle membrane / caveola / brain development / midbody / negative regulation of DNA-binding transcription factor activity / in utero embryonic development / glucose homeostasis / response to estradiol / heparin binding / postsynaptic density / protein-containing complex binding / response to drug / intracellular membrane-bounded organelle / positive regulation of transcription, DNA-templated / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / integral component of membrane / plasma membrane / nucleus / Protein patched homolog 1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.1 Å resolution
AuthorsYan, N. / Gong, X. / Qian, H.W.
CitationJournal: Science / Year: 2018
Title: Structural basis for the recognition of Sonic Hedgehog by human Patched1.
Authors: Xin Gong / Hongwu Qian / Pingping Cao / Xin Zhao / Qiang Zhou / Jianlin Lei / Nieng Yan
Abstract: The Hedgehog (Hh) pathway involved in development and regeneration is activated by the extracellular binding of Hh to the membrane receptor Patched (Ptch). We report the structures of human Ptch1 ...The Hedgehog (Hh) pathway involved in development and regeneration is activated by the extracellular binding of Hh to the membrane receptor Patched (Ptch). We report the structures of human Ptch1 alone and in complex with the N-terminal domain of human Sonic hedgehog (ShhN) at resolutions of 3.9 and 3.6 angstroms, respectively, as determined by cryo-electron microscopy. Ptch1 comprises two interacting extracellular domains, ECD1 and ECD2, and 12 transmembrane segments (TMs), with TMs 2 to 6 constituting the sterol-sensing domain (SSD). Two steroid-shaped densities are resolved in both structures, one enclosed by ECD1/2 and the other in the membrane-facing cavity of the SSD. Structure-guided mutational analysis shows that interaction between ShhN and Ptch1 is steroid-dependent. The structure of a steroid binding-deficient Ptch1 mutant displays pronounced conformational rearrangements.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 5, 2018 / Release: Jul 11, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 11, 2018Structure modelrepositoryInitial release
1.1Aug 22, 2018Structure modelData collection / Database referencescitation_citation.journal_volume

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Assembly

Deposited unit
A: Protein patched homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,8158
Polyers150,2671
Non-polymers1,5487
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide Protein patched homolog 1 / PTC1


Mass: 150266.656 Da / Num. of mol.: 1 / Mutation: L282Q, T500F, P504L / Source: (gene. exp.) Homo sapiens (human) / Gene: PTCH1, PTCH / Production host: Homo sapiens (human) / References: UniProt: Q13635
#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 7 / Formula: C8H15NO6 / N-Acetylglucosamine

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Patch1 with L282Q/T500F/P504L mutations / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameCategory
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 154721 / Symmetry type: POINT

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