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- EMDB-7968: Cryo-EM structure of human Ptch1 and ShhN complex -

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Basic information

Entry
Database: EMDB / ID: 7968
TitleCryo-EM structure of human Ptch1 and ShhN complex
Map data
SamplePatch1:
Protein patched homolog 1 / Sonic hedgehog proteinSonic hedgehog / (ligand) x 5
Function / homologyIntein N-terminal splicing motif profile. / Sterol-sensing domain / Hedgehog ligand biogenesis / Hedgehog 'off' state / Ligand-receptor interactions / Class B/2 (Secretin family receptors) / Hedgehog 'on' state / Activation of SMO / HHAT G278V abrogates palmitoylation of Hh-Np / Release of Hh-Np from the secreting cell ...Intein N-terminal splicing motif profile. / Sterol-sensing domain / Hedgehog ligand biogenesis / Hedgehog 'off' state / Ligand-receptor interactions / Class B/2 (Secretin family receptors) / Hedgehog 'on' state / Activation of SMO / HHAT G278V abrogates palmitoylation of Hh-Np / Release of Hh-Np from the secreting cell / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Protein patched/dispatched / Hint domain C-terminal / Hint domain N-terminal / Transmembrane receptor, patched / Intein N-terminal splicing region / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain superfamily / Hint module / Hedgehog amino-terminal signalling domain / Patched family / Sterol-sensing domain (SSD) profile. / regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry / neural plate axis specification / hedgehog receptor activity / cell proliferation involved in metanephros development / response to chlorate / cell differentiation involved in kidney development / smoothened signaling pathway involved in dorsal/ventral neural tube patterning / neural tube patterning / tracheoesophageal septum formation / negative regulation of ureter smooth muscle cell differentiation / positive regulation of skeletal muscle cell proliferation / positive regulation of kidney smooth muscle cell differentiation / negative regulation of kidney smooth muscle cell differentiation / positive regulation of ureter smooth muscle cell differentiation / positive regulation of sclerotome development / right lung development / left lung development / primary prostatic bud elongation / epithelial-mesenchymal signaling involved in prostate gland development / regulation of mesenchymal cell proliferation involved in prostate gland development / mesenchymal smoothened signaling pathway involved in prostate gland development / 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 / hindgut morphogenesis / polarity specification of anterior/posterior axis / striated muscle tissue development / morphogen activity / cerebellar granule cell precursor proliferation / bud outgrowth involved in lung branching / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / epidermal cell fate specification / positive regulation of immature T cell proliferation in thymus / hedgehog family protein binding / metanephric mesenchymal cell proliferation involved in metanephros development / determination of left/right asymmetry in lateral mesoderm / positive regulation of striated muscle cell differentiation / negative regulation of alpha-beta T cell differentiation / lung epithelium development / ventral midline development / positive regulation of hh target transcription factor activity / 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 / negative regulation of mesenchymal cell apoptotic process / myotube differentiation / salivary gland cavitation / intermediate filament organization / mammary gland duct morphogenesis / stem cell development / negative regulation of cholesterol efflux / pattern specification process / positive regulation of T cell differentiation in thymus / lymphoid progenitor cell differentiation / dorsal/ventral neural tube patterning / patched binding / neuroblast proliferation / negative regulation of multicellular organism growth / limb morphogenesis / somite development / negative regulation of cell division / cellular response to cholesterol / negative regulation of smoothened signaling pathway / renal system development / embryonic skeletal system development / embryonic foregut morphogenesis / embryonic digestive tract morphogenesis / limb bud formation
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsYan N / Gong X / Qian HW
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 cryo-EM structures of human ...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 cryo-EM structures of human Ptch1 alone and in complex with the N-terminal domain of human Sonic hedgehog (ShhN) at resolutions of 3.9 Å and 3.6 Å, respectively. Ptch1 comprises two interacting extracellular domains ECD1 and ECD2 and twelve transmembrane segments (TMs), with TMs 2-6 constituting the sterol-sensing domain (SSD). Two steroid-shaped densities are resolved in both structures, one enclosed by ECD1/2, and the other on the membrane-facing cavity of 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 ReportPDB-ID: 6dmy

SummaryFull reportAbout validation report
DateDeposition: Jun 5, 2018 / Header (metadata) release: Jul 11, 2018 / Map release: Jul 11, 2018 / Last update: Jul 11, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6dmy
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7968.map.gz (map file in CCP4 format, 44958 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
224 pix
1.09 Å/pix.
= 244.384 Å
224 pix
1.09 Å/pix.
= 244.384 Å
224 pix
1.09 Å/pix.
= 244.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.11725369 - 0.21128653
Average (Standard dev.)0.00041769576 (0.0074620936)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions224224224
Origin0.0.0.
Limit223.223.223.
Spacing224224224
CellA=B=C: 244.38399 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z244.384244.384244.384
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.1170.2110.000

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Supplemental data

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Sample components

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Entire Patch1

EntireName: Patch1 / Number of components: 8

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Component #1: cellular-component, Patch1

Cellular-componentName: Patch1 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Protein patched homolog 1

ProteinName: Protein patched homolog 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 150.189578 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Sonic hedgehog protein

ProteinName: Sonic hedgehog proteinSonic hedgehog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.934461 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #4: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #5: ligand, CHOLESTEROL HEMISUCCINATE

LigandName: CHOLESTEROL HEMISUCCINATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.486726 kDa

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Component #6: ligand, SERINE

LigandName: SERINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.105093 kDa

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Component #7: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #8: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 15 mg/ml / pH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 137823
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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