[English] 日本語
- PDB-6dmb: Cryo-EM structure of human Ptch1 -

Open data

ID or keywords:


no data

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) / Sterol-sensing domain (SSD) profile. / Patched family / Transmembrane receptor, patched / Protein patched/dispatched / Activation of SMO / Hedgehog 'on' state / Sterol-sensing domain / Hedgehog 'off' state / Ligand-receptor interactions ...Class B/2 (Secretin family receptors) / Sterol-sensing domain (SSD) profile. / Patched family / Transmembrane receptor, patched / Protein patched/dispatched / Activation of SMO / Hedgehog 'on' state / Sterol-sensing domain / Hedgehog 'off' state / Ligand-receptor interactions / hedgehog receptor activity / neural plate axis specification / response to chlorate / 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 / somite development / limb morphogenesis / negative regulation of multicellular organism growth / negative regulation of cell division / negative regulation of smoothened signaling pathway / cellular response to cholesterol / positive regulation of cholesterol efflux / renal system development / keratinocyte proliferation / dorsal/ventral pattern formation / pharyngeal system development / positive regulation of epidermal cell differentiation / mammary gland epithelial cell differentiation / cell fate determination / commissural neuron axon guidance / 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 / negative regulation of epithelial cell proliferation / dendritic growth cone / protein localization to plasma membrane / axonal growth cone / protein processing / cyclin binding / 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 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 4, 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

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7963
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:

Downloads & links


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

About Yorodumi


Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more