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- PDB-6dmb: Cryo-EM structure of human Ptch1 -

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Basic information

Database: PDB / ID: 6dmb
TitleCryo-EM structure of human Ptch1
ComponentsProtein patched homolog 1
KeywordsPROTEIN BINDING / Receptor / RND family
Function / homologyClass B/2 (Secretin family receptors) / Activation of SMO / Hedgehog 'off' state / Sterol-sensing domain / Hedgehog 'on' state / Ligand-receptor interactions / Sterol-sensing domain (SSD) profile. / Protein patched/dispatched / Transmembrane receptor, patched / Patched family ...Class B/2 (Secretin family receptors) / Activation of SMO / Hedgehog 'off' state / Sterol-sensing domain / Hedgehog 'on' state / Ligand-receptor interactions / Sterol-sensing domain (SSD) profile. / Protein patched/dispatched / Transmembrane receptor, patched / Patched family / neural plate axis specification / response to chlorate / hedgehog receptor activity / 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 / negative regulation of multicellular organism growth / somite development / limb morphogenesis / negative regulation of cell division / cellular response to cholesterol / negative regulation of smoothened signaling pathway / renal system development / positive regulation of cholesterol efflux / keratinocyte proliferation / pharyngeal system development / dorsal/ventral pattern formation / commissural neuron axon guidance / positive regulation of epidermal cell differentiation / mammary gland epithelial cell differentiation / cell fate determination / 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 / heart morphogenesis / dendritic growth cone / negative regulation of epithelial cell proliferation / axonal growth cone / protein localization to plasma membrane / cyclin binding / protein processing / response to retinoic acid / animal organ morphogenesis / regulation of protein localization / neural tube closure / response to mechanical stimulus / liver regeneration / regulation of mitotic cell cycle / 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 / 3.9 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 cryo-EM structures of human ...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 cryo-EM structures of human Ptch1 alone and in complex with the N-terminal domain of human Sonic hedgehog (ShhN) at resolutions of 3.9 Å and 3.6 Å, respectively. Ptch1 comprises two interacting extracellular domains ECD1 and ECD2 and twelve transmembrane segments (TMs), with TMs 2-6 constituting the sterol-sensing domain (SSD). Two steroid-shaped densities are resolved in both structures, one enclosed by ECD1/2, and the other on the membrane-facing cavity of 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 4, 2018 / Release: Jul 11, 2018

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Deposited unit
A: Protein patched homolog 1
hetero molecules

Theoretical massNumber of molelcules
Total (without water)152,71110

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


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

Mass: 150189.578 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PTCH1, PTCH / Production host: Homo sapiens (human) / References: UniProt: Q13635
#2: Chemical

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

Mass: 486.726 Da / Num. of mol.: 2 / Formula: C31H50O4

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: Patch1 / 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

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)


SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 94445 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0088151
ELECTRON MICROSCOPYf_angle_d1.30511112
ELECTRON MICROSCOPYf_dihedral_angle_d11.2374803
ELECTRON MICROSCOPYf_chiral_restr0.0671291
ELECTRON MICROSCOPYf_plane_restr0.0091383

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