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- EMDB-0355: Cryo-EM structure of tetrameric Ptch1 in complex with ShhNp (form I) -

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Basic information

Entry
Database: EMDB / ID: EMD-0355
TitleCryo-EM structure of tetrameric Ptch1 in complex with ShhNp (form I)
Map data
SamplePatch1:
Protein patched homolog 1 / Sonic hedgehog proteinSonic hedgehog / (ligand) x 5
Function / homology
Function and homology information


Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Hedgehog 'on' state / Activation of SMO / HHAT G278V abrogates palmitoylation of Hh-Np / Class B/2 (Secretin family receptors) / Release of Hh-Np from the secreting cell / Hedgehog ligand biogenesis / Hedgehog 'off' state / Ligand-receptor interactions / regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry ...Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Hedgehog 'on' state / Activation of SMO / HHAT G278V abrogates palmitoylation of Hh-Np / Class B/2 (Secretin family receptors) / Release of Hh-Np from the secreting cell / Hedgehog ligand biogenesis / Hedgehog 'off' state / Ligand-receptor interactions / regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry / cell proliferation involved in metanephros development / neural plate axis specification / hedgehog receptor activity / response to chlorate / cell differentiation involved in kidney development / smoothened signaling pathway involved in dorsal/ventral neural tube patterning / right lung development / positive regulation of skeletal muscle cell proliferation / positive regulation of kidney smooth muscle cell differentiation / negative regulation of kidney smooth muscle cell differentiation / negative regulation of ureter smooth muscle cell differentiation / tracheoesophageal septum formation / left lung development / regulation of mesenchymal cell proliferation involved in prostate gland development / positive regulation of sclerotome development / mesenchymal smoothened signaling pathway involved in prostate gland development / epithelial-mesenchymal signaling involved in prostate gland development / primary prostatic bud elongation / positive regulation of ureter smooth muscle cell differentiation / regulation of odontogenesis / regulation of prostatic bud formation / neural tube patterning / positive regulation of mesenchymal cell proliferation involved in ureter development / spinal cord dorsal/ventral patterning / smoothened binding / hindgut morphogenesis / morphogen activity / polarity specification of anterior/posterior axis / cerebellar granule cell precursor proliferation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / striated muscle tissue development / positive regulation of immature T cell proliferation in thymus / bud outgrowth involved in lung branching / epidermal cell fate specification / metanephric mesenchymal cell proliferation involved in metanephros development / positive regulation of striated muscle cell differentiation / hedgehog family protein binding / negative regulation of alpha-beta T cell differentiation / determination of left/right asymmetry in lateral mesoderm / positive regulation of hh target transcription factor activity / ventral midline development / 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 / laminin-1 binding / spinal cord motor neuron differentiation / stem cell development / negative regulation of mesenchymal cell apoptotic process / salivary gland cavitation / myotube differentiation / intermediate filament organization / mammary gland duct morphogenesis / positive regulation of T cell differentiation in thymus / neuroblast proliferation / negative regulation of cholesterol efflux / renal system development / limb morphogenesis / dorsal/ventral neural tube patterning / patched binding / somite development / negative regulation of transcription elongation from RNA polymerase II promoter / cellular response to cholesterol / keratinocyte proliferation / negative regulation of cell division / embryonic digestive tract morphogenesis / lymphoid progenitor cell differentiation / lung lobe morphogenesis / negative regulation of smoothened signaling pathway / limb bud formation / embryonic foregut morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / negative thymic T cell selection / embryonic skeletal system development / negative regulation of multicellular organism growth / pharyngeal system development / hindbrain development / dorsal/ventral pattern formation / mesenchymal cell proliferation involved in lung development / thalamus development / negative regulation of dopaminergic neuron differentiation / animal organ formation / male genitalia development / positive regulation of epidermal cell differentiation / mammary gland epithelial cell differentiation / metanephros development / ectoderm development
Patched family / Sterol-sensing domain / Intein N-terminal splicing motif profile. / Sterol-sensing domain (SSD) profile. / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Protein patched/dispatched / Hint domain C-terminal / Hint domain N-terminal ...Patched family / Sterol-sensing domain / Intein N-terminal splicing motif profile. / Sterol-sensing domain (SSD) profile. / 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
Protein patched homolog 1 / Sonic hedgehog protein
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsYan N / Gong X / Qian HW
CitationJournal: To Be Published
Title: Cryo-EM structure of the 2:1 hPtch1-Shhp complex
Authors: Yan N / Gong X / Qian HW
Validation ReportPDB-ID: 6n7g

SummaryFull reportAbout validation report
DateDeposition: Nov 27, 2018 / Header (metadata) release: May 29, 2019 / Map release: May 29, 2019 / Update: May 29, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6n7g
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6n7g
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0355.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 280 pix.
= 311.92 Å
1.11 Å/pix.
x 280 pix.
= 311.92 Å
1.11 Å/pix.
x 280 pix.
= 311.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.114 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.017574318 - 0.07663275
Average (Standard dev.)0.00065977516 (±0.00578557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 311.91998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1141.1141.114
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z311.920311.920311.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0180.0770.001

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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: 4 / 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: 2 / Recombinant expression: No
MassTheoretical: 19.594039 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 28 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #5: ligand, CHOLESTEROL

LigandName: CHOLESTEROL / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 0.386654 kDa

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Component #6: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #7: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Component #8: ligand, PALMITIC ACID

LigandName: PALMITIC ACID / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.256424 kDa

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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: 50 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: 39503
3D reconstructionSoftware: RELION / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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