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- EMDB-7796: Structure of human Patched1 in complex with native Sonic Hedgehog -

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Basic information

Entry
Database: EMDB / ID: 7796
TitleStructure of human Patched1 in complex with native Sonic Hedgehog
Map dataA protein structure
SamplePtc:
Protein patched homolog 1 / Sonic hedgehog proteinSonic hedgehog / (ligand) x 3
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 / 3.5 Å resolution
AuthorsQi X / Li X
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 ReportPDB-ID: 6d4j

SummaryFull reportAbout validation report
DateDeposition: Apr 18, 2018 / Header (metadata) release: Jul 4, 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: 0.55
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6d4j
  • Surface level: 0.5
  • 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_7796.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1 Å/pix.
= 256. Å
256 pix
1 Å/pix.
= 256. Å
256 pix
1 Å/pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density
Contour Level:0.55 (by emdb), 0.55 (movie #1):
Minimum - Maximum-1.3252866 - 2.2768981
Average (Standard dev.)0.0033889343 (0.08910678)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.0.0.
Limit255.255.255.
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.3252.2770.003

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Supplemental data

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Sample components

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Entire Ptc

EntireName: Ptc / Number of components: 6

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Component #1: protein, Ptc

ProteinName: Ptc / Recombinant expression: No
MassExperimental: 121 kDa
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: 160.714406 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: 19.594039 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: 6 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #5: ligand, ZINC ION

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

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Component #6: ligand, PALMITIC ACID

LigandName: PALMITIC ACID / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.256424 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionpH: 7
VitrificationCryogen name: NONE

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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: 1.6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: DARK FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 789118
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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