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- PDB-6dmy: Cryo-EM structure of human Ptch1 and ShhN complex -

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Entry
Database: PDB / ID: 6dmy
TitleCryo-EM structure of human Ptch1 and ShhN complex
Components
  • Protein patched homolog 1
  • Sonic hedgehog proteinSonic hedgehog
KeywordsPROTEIN BINDING / Receptor / RND family
Function / homologyPatched family / Sterol-sensing domain / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Hedgehog ligand biogenesis / Hedgehog 'off' state / Ligand-receptor interactions / Activation of SMO / HHAT G278V abrogates palmitoylation of Hh-Np / Intein N-terminal splicing motif profile. / Class B/2 (Secretin family receptors) ...Patched family / Sterol-sensing domain / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Hedgehog ligand biogenesis / Hedgehog 'off' state / Ligand-receptor interactions / Activation of SMO / HHAT G278V abrogates palmitoylation of Hh-Np / Intein N-terminal splicing motif profile. / Class B/2 (Secretin family receptors) / Hedgehog, N-terminal signalling domain / Sterol-sensing domain (SSD) profile. / Hedgehog 'on' state / Release of Hh-Np from the secreting cell / Transmembrane receptor, patched / Hedgehog amino-terminal signalling domain / Hedgehog protein / Hint domain superfamily / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Intein N-terminal splicing region / Hint module / Hint domain N-terminal / Hint domain C-terminal / Protein patched/dispatched / Hedgehog protein, Hint domain / regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry / neural plate axis specification / cell proliferation involved in metanephros development / hedgehog receptor activity / cell differentiation involved in kidney development / smoothened signaling pathway involved in dorsal/ventral neural tube patterning / response to chlorate / positive regulation of sclerotome development / regulation of mesenchymal cell proliferation involved in prostate gland development / epithelial-mesenchymal signaling involved in prostate gland development / mesenchymal smoothened signaling pathway involved in prostate gland development / left lung development / positive regulation of skeletal muscle cell proliferation / primary prostatic bud elongation / tracheoesophageal septum formation / negative regulation of ureter smooth muscle cell differentiation / positive regulation of ureter smooth muscle cell differentiation / negative regulation of kidney smooth muscle cell differentiation / positive regulation of kidney smooth muscle cell differentiation / right lung development / neural tube patterning / regulation of odontogenesis / regulation of prostatic bud formation / positive regulation of mesenchymal cell proliferation involved in ureter development / spinal cord dorsal/ventral patterning / hindgut morphogenesis / polarity specification of anterior/posterior axis / morphogen activity / smoothened binding / cerebellar granule cell precursor proliferation / bud outgrowth involved in lung branching / striated muscle tissue development / positive regulation of immature T cell proliferation in thymus / epidermal cell fate specification / metanephric mesenchymal cell proliferation involved in metanephros development / positive regulation of hh target transcription factor activity / positive regulation of striated muscle cell differentiation / negative regulation of alpha-beta T cell differentiation / hedgehog family protein binding / determination of left/right asymmetry in lateral mesoderm / ventral midline development / lung epithelium development / artery development / smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation / formation of anatomical boundary / hindlimb morphogenesis / trachea morphogenesis / telencephalon regionalization / spinal cord motor neuron differentiation / laminin-1 binding / stem cell development / negative regulation of mesenchymal cell apoptotic process / myotube differentiation / salivary gland cavitation / intermediate filament organization / mammary gland duct morphogenesis / positive regulation of T cell differentiation in thymus / negative regulation of cholesterol efflux / neuroblast proliferation / dorsal/ventral neural tube patterning / patched binding / limb morphogenesis / somite development / cellular response to cholesterol / negative regulation of smoothened signaling pathway / negative regulation of cell division / negative regulation of transcription elongation from RNA polymerase II promoter / keratinocyte proliferation / renal system development / lymphoid progenitor cell differentiation / embryonic digestive tract morphogenesis / negative regulation of multicellular organism growth / embryonic foregut morphogenesis / limb bud formation / lung lobe morphogenesis
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 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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Structure visualization

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Assembly

Deposited unit
A: Protein patched homolog 1
B: Sonic hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,89715
Polyers170,1242
Non-polymers2,77313
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein/peptide , 2 types, 2 molecules AB

#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: Protein/peptide Sonic hedgehog protein / Sonic hedgehog / SHH / HHG-1 / Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains / ShhNC


Mass: 19934.461 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SHH
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q15465

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Non-polymers , 5 types, 13 molecules

#3: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 7 / Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Formula: C31H50O4
#5: Chemical ChemComp-SER / SERINE


Mass: 105.093 Da / Num. of mol.: 1 / Formula: C3H7NO3 / Serine
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium

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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 / 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 / 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 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11rc3_2542: / Classification: refinement
EM software
IDNameCategory
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.6 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 137823 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0099418
ELECTRON MICROSCOPYf_angle_d1.36612821
ELECTRON MICROSCOPYf_dihedral_angle_d11.6685564
ELECTRON MICROSCOPYf_chiral_restr0.0711467
ELECTRON MICROSCOPYf_plane_restr0.0091607

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