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- PDB-6d4h: Structure of human Patched1 -

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Basic information

Entry
Database: PDB / ID: 6d4h
TitleStructure of human Patched1
ComponentsProtein patched homolog 1
KeywordsMEMBRANE PROTEIN / tumor suppressor
Function / homologySterol-sensing domain (SSD) profile. / Patched family / Transmembrane receptor, patched / Protein patched/dispatched / Sterol-sensing domain / Activation of SMO / Hedgehog 'on' state / Class B/2 (Secretin family receptors) / Ligand-receptor interactions / Hedgehog 'off' state ...Sterol-sensing domain (SSD) profile. / Patched family / Transmembrane receptor, patched / Protein patched/dispatched / Sterol-sensing domain / Activation of SMO / Hedgehog 'on' state / Class B/2 (Secretin family receptors) / Ligand-receptor interactions / Hedgehog 'off' state / hedgehog receptor activity / response to chlorate / neural plate axis specification / 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 / limb morphogenesis / somite development / cellular response to cholesterol / negative regulation of smoothened signaling pathway / negative regulation of cell division / keratinocyte proliferation / renal system development / negative regulation of multicellular organism growth / positive regulation of cholesterol efflux / pharyngeal system development / dorsal/ventral pattern formation / positive regulation of epidermal cell differentiation / mammary gland epithelial cell differentiation / cell fate determination / commissural neuron axon guidance / smoothened signaling pathway / ciliary membrane / prostate gland development / regulation of smoothened signaling pathway / embryonic organ development / embryonic limb morphogenesis / cholesterol binding / negative regulation of osteoblast differentiation / regulation of mitotic cell cycle / branching involved in ureteric bud morphogenesis / negative regulation of epithelial cell proliferation / dendritic growth cone / heart morphogenesis / axonal growth cone / protein processing / cyclin binding / protein localization to plasma membrane / response to retinoic acid / regulation of protein localization / liver regeneration / neural tube closure / response to mechanical stimulus / animal organ morphogenesis / endocytic vesicle membrane / caveola / brain development / midbody / negative regulation of DNA-binding transcription factor activity / glucose homeostasis / in utero embryonic development / response to estradiol / heparin binding / postsynaptic density / protein-containing complex binding / response to drug / intracellular membrane-bounded organelle / positive regulation of transcription, DNA-templated / negative regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / integral component of membrane / plasma membrane / nucleus / Protein patched homolog 1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / 3.5 Å resolution
AuthorsQi, X. / Li, X. / Wang, J.
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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Structure visualization

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Assembly

Deposited unit
A: Protein patched homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,4819
Polyers161,7111
Non-polymers1,7708
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 161711.406 Da / Num. of mol.: 1 / 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.: 8 / 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: Ptc / Type: COMPLEX / Entity ID: 1 / 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: 0.766 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 99.788 / Overall SU ML: 1.282 / Overall ESU R: 1.81
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: 123.999 Å2 / Aniso B11: -3.34 Å2 / Aniso B12: -0.36 Å2 / Aniso B13: -1.76 Å2 / Aniso B22: 1.11 Å2 / Aniso B23: 0.51 Å2 / Aniso B33: 2.24 Å2
Least-squares processR factor R work: 0.46768 / R factor obs: 0.46768 / Highest resolution: 3.5 Å / Lowest resolution: 78.2 Å / Number reflection obs: 35251 / Percent reflection obs: 1
Refine hist #1Highest resolution: 3.5 Å / Lowest resolution: 78.2 Å
Number of atoms included #1Total: 7317
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0147477
ELECTRON MICROSCOPYr_bond_other_d0.0040.0177022
ELECTRON MICROSCOPYr_angle_refined_deg1.1551.65010187
ELECTRON MICROSCOPYr_angle_other_deg0.9661.64716242
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.7195.000961
ELECTRON MICROSCOPYr_dihedral_angle_2_deg28.35322.097310
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.68215.0001116
ELECTRON MICROSCOPYr_dihedral_angle_4_deg9.60415.00033
ELECTRON MICROSCOPYr_chiral_restr0.0550.2001028
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.0208396
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0201460
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_it1.69612.8803852
ELECTRON MICROSCOPYr_mcbond_other1.69512.8803851
ELECTRON MICROSCOPYr_mcangle_it3.11219.3214810
ELECTRON MICROSCOPYr_mcangle_other3.11119.3214811
ELECTRON MICROSCOPYr_scbond_it10.40112.8353625
ELECTRON MICROSCOPYr_scbond_other10.40012.8363626
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other12.19219.1775378
ELECTRON MICROSCOPYr_long_range_B_refined7.9908796
ELECTRON MICROSCOPYr_long_range_B_other7.9908797
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.5 Å / R factor R free: 0 / R factor R work: 0.681 / Lowest resolution: 3.591 Å / Number reflection R free: 0 / Number reflection R work: 2611 / Total number of bins used: 20 / Percent reflection obs: 1

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