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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 / homologySterol-sensing domain (SSD) profile. / Hedgehog protein / Hedgehog 'off' state / Ligand-receptor interactions / Release of Hh-Np from the secreting cell / Hedgehog 'on' state / Activation of SMO / HHAT G278V abrogates palmitoylation of Hh-Np / Class B/2 (Secretin family receptors) / Hedgehog ligand biogenesis ...Sterol-sensing domain (SSD) profile. / Hedgehog protein / Hedgehog 'off' state / Ligand-receptor interactions / Release of Hh-Np from the secreting cell / Hedgehog 'on' state / Activation of SMO / HHAT G278V abrogates palmitoylation of Hh-Np / Class B/2 (Secretin family receptors) / Hedgehog ligand biogenesis / Hedgehog, N-terminal signalling domain / Intein N-terminal splicing motif profile. / Sterol-sensing domain / 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 / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry / response to chlorate / hedgehog receptor activity / neural plate axis specification / cell proliferation involved in metanephros development / smoothened signaling pathway involved in dorsal/ventral neural tube patterning / cell differentiation involved in kidney development / neural tube patterning / left lung development / regulation of mesenchymal cell proliferation involved in prostate gland development / right lung development / negative regulation of kidney smooth muscle cell differentiation / primary prostatic bud elongation / epithelial-mesenchymal signaling involved in prostate gland development / positive regulation of ureter smooth muscle cell differentiation / mesenchymal smoothened signaling pathway involved in prostate gland development / positive regulation of skeletal muscle cell proliferation / negative regulation of ureter smooth muscle cell differentiation / positive regulation of sclerotome development / tracheoesophageal septum formation / positive regulation of kidney smooth muscle cell differentiation / regulation of odontogenesis / regulation of prostatic bud formation / smoothened binding / 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 / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / cerebellar granule cell precursor proliferation / epidermal cell fate specification / bud outgrowth involved in lung branching / morphogen activity / hedgehog family protein binding / positive regulation of immature T cell proliferation in thymus / metanephric mesenchymal cell proliferation involved in metanephros development / positive regulation of striated muscle cell differentiation / negative regulation of alpha-beta T cell differentiation / determination of left/right asymmetry in lateral mesoderm / ventral midline development / positive regulation of hh target transcription factor activity / artery development / lung epithelium development / formation of anatomical boundary / smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation / hindlimb morphogenesis / trachea morphogenesis / telencephalon regionalization / spinal cord motor neuron differentiation / laminin-1 binding / negative regulation of mesenchymal cell apoptotic process / salivary gland cavitation / myotube differentiation / stem cell development / intermediate filament organization / mammary gland duct morphogenesis / pattern specification process / positive regulation of T cell differentiation in thymus / dorsal/ventral neural tube patterning / negative regulation of cholesterol efflux / patched binding / neuroblast proliferation / lymphoid progenitor cell differentiation / limb morphogenesis / somite development / negative regulation of multicellular organism growth / 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 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 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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