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- PDB-6d4j: Structure of human Patched1 in complex with native Sonic Hedgehog -

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Basic information

Entry
Database: PDB / ID: 6d4j
TitleStructure of human Patched1 in complex with native Sonic Hedgehog
Components
  • Protein patched homolog 1
  • Sonic hedgehog proteinSonic hedgehog
KeywordsMEMBRANE PROTEIN / tumor suppressor / Hh
Function / homologyIntein N-terminal splicing motif profile. / Hedgehog protein / Release of Hh-Np from the secreting cell / Hedgehog ligand biogenesis / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Ligand-receptor interactions / Hedgehog 'on' state / Activation of SMO / HHAT G278V abrogates palmitoylation of Hh-Np / Hedgehog, N-terminal signalling domain ...Intein N-terminal splicing motif profile. / Hedgehog protein / Release of Hh-Np from the secreting cell / Hedgehog ligand biogenesis / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Ligand-receptor interactions / Hedgehog 'on' state / Activation of SMO / HHAT G278V abrogates palmitoylation of Hh-Np / Hedgehog, N-terminal signalling domain / Sterol-sensing domain / Class B/2 (Secretin family receptors) / Hedgehog 'off' state / Hedgehog protein, Hint domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Sterol-sensing domain (SSD) profile. / Patched family / Protein patched/dispatched / Hint module / Hint domain superfamily / Hedgehog amino-terminal signalling domain / Intein N-terminal splicing region / Hint domain C-terminal / Transmembrane receptor, patched / Hint domain N-terminal / regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry / hedgehog receptor activity / response to chlorate / neural plate axis specification / cell proliferation involved in metanephros development / smoothened signaling pathway involved in dorsal/ventral neural tube patterning / cell differentiation involved in kidney development / neural tube patterning / mesenchymal smoothened signaling pathway involved in prostate gland development / positive regulation of kidney smooth muscle cell differentiation / positive regulation of skeletal muscle cell proliferation / positive regulation of sclerotome development / right lung development / negative regulation of ureter smooth muscle cell differentiation / left lung development / positive regulation of ureter smooth muscle cell differentiation / negative regulation of kidney smooth muscle cell differentiation / tracheoesophageal septum formation / regulation of mesenchymal cell proliferation involved in prostate gland development / epithelial-mesenchymal signaling involved in prostate gland development / primary prostatic bud elongation / smoothened binding / regulation of prostatic bud formation / regulation of odontogenesis / positive regulation of mesenchymal cell proliferation involved in ureter development / spinal cord dorsal/ventral patterning / morphogen activity / polarity specification of anterior/posterior axis / hindgut morphogenesis / bud outgrowth involved in lung branching / epidermal cell fate specification / striated muscle tissue development / cerebellar granule cell precursor proliferation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / positive regulation of immature T cell proliferation in thymus / hedgehog family protein binding / metanephric mesenchymal cell proliferation involved in metanephros development / positive regulation of striated muscle cell differentiation / negative regulation of alpha-beta T cell differentiation / determination of left/right asymmetry in lateral mesoderm / ventral midline development / positive regulation of hh target transcription factor activity / lung epithelium development / artery development / formation of anatomical boundary / smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation / hindlimb morphogenesis / trachea morphogenesis / telencephalon regionalization / spinal cord motor neuron differentiation / laminin-1 binding / negative regulation of mesenchymal cell apoptotic process / myotube differentiation / salivary gland cavitation / mammary gland duct morphogenesis / stem cell development / intermediate filament organization / pattern specification process / positive regulation of T cell differentiation in thymus / dorsal/ventral neural tube patterning / negative regulation of cholesterol efflux / patched binding / neuroblast proliferation / lymphoid progenitor cell differentiation / embryonic foregut morphogenesis / somite development / negative regulation of multicellular organism growth / limb morphogenesis / hindbrain development / negative regulation of cell division / cellular response to cholesterol / negative regulation of smoothened signaling pathway / renal system development / mesenchymal cell proliferation involved in lung development / embryonic skeletal system development
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / 3.5 Å resolution
AuthorsQi, X. / Li, X.
CitationJournal: Nature / Year: 2018
Title: Structures of human Patched and its complex with native palmitoylated sonic hedgehog.
Authors: Xiaofeng Qi / Philip Schmiege / Elias Coutavas / Jiawei Wang / Xiaochun Li
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 18, 2018 / Release: Jul 11, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 11, 2018Structure modelrepositoryInitial release
1.1Jul 25, 2018Structure modelData collection / Database referencescitation_citation.pdbx_database_id_PubMed / _citation.title
1.2Aug 15, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)181,95810
Polyers180,3082
Non-polymers1,6498
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 160714.406 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: 19594.039 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SHH / Production host: Homo sapiens (human) / References: UniProt: Q15465
#3: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 6 / Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#5: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Formula: C16H32O2 / Palmitic acid

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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: Ptc / Type: COMPLEX / Entity ID: 1,2 / Source: RECOMBINANT
Molecular weightValue: 0.121 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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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: DARK FIELD
Image recordingElectron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0222 / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 789118 / Symmetry type: POINT
RefineCorrelation coeff Fo to Fc: 0.814 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 102.448 / Overall SU ML: 1.185 / Overall ESU R: 1.39
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 178.787 Å2 / Aniso B11: -0.69 Å2 / Aniso B12: -0.36 Å2 / Aniso B13: -1.18 Å2 / Aniso B22: 0.32 Å2 / Aniso B23: 0.69 Å2 / Aniso B33: 0.37 Å2
Least-squares processR factor R work: 0.44768 / R factor obs: 0.44768 / Highest resolution: 3.8 Å / Lowest resolution: 83.4 Å / Number reflection obs: 47359 / Percent reflection obs: 99.99
Number of atoms included #1Total: 8613
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0148800
ELECTRON MICROSCOPYr_bond_other_d0.0040.0178209
ELECTRON MICROSCOPYr_angle_refined_deg1.0471.64911962
ELECTRON MICROSCOPYr_angle_other_deg0.8461.64819037
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.8585.0001125
ELECTRON MICROSCOPYr_dihedral_angle_2_deg28.78421.830388
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.97415.0001350
ELECTRON MICROSCOPYr_dihedral_angle_4_deg10.99815.00046
ELECTRON MICROSCOPYr_chiral_restr0.0450.2001186
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.0209910
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0201706
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.84618.3714511
ELECTRON MICROSCOPYr_mcbond_other2.84518.3694510
ELECTRON MICROSCOPYr_mcangle_it5.15427.5565632
ELECTRON MICROSCOPYr_mcangle_other5.15427.5585633
ELECTRON MICROSCOPYr_scbond_it5.26218.6734289
ELECTRON MICROSCOPYr_scbond_other5.26318.6704287
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other6.94727.8686330
ELECTRON MICROSCOPYr_long_range_B_refined9.82210266
ELECTRON MICROSCOPYr_long_range_B_other9.82210267
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.8 Å / R factor R free: 0 / R factor R work: 0.581 / Lowest resolution: 3.898 Å / Number reflection R free: 0 / Number reflection R work: 3453 / Total number of bins used: 20 / Percent reflection obs: 99.97

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