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- PDB-9ms8: PTCH1 in complex with Fab6H3 -

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Basic information

Entry
Database: PDB / ID: 9ms8
TitlePTCH1 in complex with Fab6H3
Components
  • 6H3 Fab heavy chain
  • 6H3 Fab light chain
  • Protein patched homolog 1
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / PTCH1 / Antibody / hedgehog signaling / cryo-EM / membrane protein. / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


neural plate axis specification / cell differentiation involved in kidney development / hedgehog receptor activity / response to chlorate / neural tube patterning / cell proliferation involved in metanephros development / smoothened binding / hedgehog family protein binding / hindlimb morphogenesis / Ligand-receptor interactions ...neural plate axis specification / cell differentiation involved in kidney development / hedgehog receptor activity / response to chlorate / neural tube patterning / cell proliferation involved in metanephros development / smoothened binding / hedgehog family protein binding / hindlimb morphogenesis / Ligand-receptor interactions / epidermal cell fate specification / spinal cord motor neuron differentiation / prostate gland development / limb morphogenesis / Activation of SMO / negative regulation of cell division / patched binding / somite development / dorsal/ventral neural tube patterning / smooth muscle tissue development / cellular response to cholesterol / pharyngeal system development / mammary gland duct morphogenesis / mammary gland epithelial cell differentiation / cell fate determination / commissural neuron axon guidance / metanephric collecting duct development / regulation of smoothened signaling pathway / dorsal/ventral pattern formation / Class B/2 (Secretin family receptors) / embryonic limb morphogenesis / negative regulation of multicellular organism growth / ciliary membrane / cholesterol binding / branching involved in ureteric bud morphogenesis / smoothened signaling pathway / positive regulation of epidermal cell differentiation / spermatid development / dendritic growth cone / keratinocyte proliferation / positive regulation of cholesterol efflux / negative regulation of osteoblast differentiation / negative regulation of keratinocyte proliferation / embryonic organ development / response to retinoic acid / axonal growth cone / heart morphogenesis / negative regulation of stem cell proliferation / Hedgehog 'off' state / response to mechanical stimulus / cyclin binding / regulation of mitotic cell cycle / liver regeneration / animal organ morphogenesis / protein localization to plasma membrane / stem cell proliferation / negative regulation of smoothened signaling pathway / negative regulation of DNA-binding transcription factor activity / neural tube closure / Hedgehog 'on' state / brain development / protein processing / caveola / endocytic vesicle membrane / apical part of cell / glucose homeostasis / response to estradiol / heparin binding / regulation of protein localization / midbody / in utero embryonic development / postsynaptic membrane / response to xenobiotic stimulus / intracellular membrane-bounded organelle / protein-containing complex binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
Transmembrane receptor, patched / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
Similarity search - Domain/homology
Protein patched homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsHu, Q. / Qi, X. / Li, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149533 United States
CitationJournal: Cell Discov / Year: 2025
Title: Inhibiting hedgehog signal by a patched-1 antibody.
Authors: Qinli Hu / Xiaofeng Qi / Linda Donnelly / Xiaochun Li /
History
DepositionJan 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein patched homolog 1
L: 6H3 Fab light chain
H: 6H3 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)145,4113
Polymers145,4113
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 122175.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTCH1, PTCH / Production host: Homo sapiens (human) / References: UniProt: Q13635
#2: Antibody 6H3 Fab light chain


Mass: 10968.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody 6H3 Fab heavy chain


Mass: 12267.724 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PTCH1 in complex with Fab6H3 / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Buffer solutionpH: 7.5
SpecimenEmbedding 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
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 258693 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039523
ELECTRON MICROSCOPYf_angle_d0.72612948
ELECTRON MICROSCOPYf_dihedral_angle_d6.1431321
ELECTRON MICROSCOPYf_chiral_restr0.0431464
ELECTRON MICROSCOPYf_plane_restr0.0051628

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