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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: EMD-7968
TitleCryo-EM structure of human Ptch1 and ShhN complex
Map data
Sample
  • Organelle or cellular component: Patch1
    • Protein or peptide: Protein patched homolog 1
  • Protein or peptide: Sonic hedgehog protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: SERINE
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
KeywordsReceptor / RND family / PROTEIN BINDING
Function / homology
Function and homology information


positive regulation of skeletal muscle cell proliferation / neural plate axis specification / right lung development / left lung development / primary prostatic bud elongation / regulation of mesenchymal cell proliferation involved in prostate gland development / mesenchymal smoothened signaling pathway involved in prostate gland development / positive regulation of sclerotome development / tracheoesophageal septum formation / negative regulation of ureter smooth muscle cell differentiation ...positive regulation of skeletal muscle cell proliferation / neural plate axis specification / right lung development / left lung development / primary prostatic bud elongation / regulation of mesenchymal cell proliferation involved in prostate gland development / mesenchymal smoothened signaling pathway involved in prostate gland development / positive regulation of sclerotome development / tracheoesophageal septum formation / negative regulation of ureter smooth muscle cell differentiation / positive regulation of ureter smooth muscle cell differentiation / negative regulation of kidney smooth muscle cell differentiation / positive regulation of kidney smooth muscle cell differentiation / morphogen activity / regulation of odontogenesis / cell differentiation involved in kidney development / positive regulation of mesenchymal cell proliferation involved in ureter development / hedgehog receptor activity / response to chlorate / neural tube patterning / trunk neural crest cell migration / Formation of lateral plate mesoderm / cell proliferation involved in metanephros development / hindgut morphogenesis / polarity specification of anterior/posterior axis / striated muscle tissue development / negative regulation of alpha-beta T cell differentiation / regulation of glial cell proliferation / regulation of prostatic bud formation / metanephric mesenchymal cell proliferation involved in metanephros development / smoothened binding / formation of anatomical boundary / lung epithelium development / positive regulation of striated muscle cell differentiation / ventral midline development / hedgehog family protein binding / trachea morphogenesis / cholesterol-protein transferase activity / bud outgrowth involved in lung branching / HHAT G278V doesn't palmitoylate Hh-Np / telencephalon regionalization / epithelial-mesenchymal cell signaling / Ligand-receptor interactions / laminin-1 binding / hindlimb morphogenesis / limb bud formation / lung lobe morphogenesis / negative regulation of cholesterol efflux / limb morphogenesis / salivary gland cavitation / spinal cord dorsal/ventral patterning / negative regulation of mesenchymal cell apoptotic process / determination of left/right asymmetry in lateral mesoderm / embryonic digestive tract morphogenesis / positive regulation of cerebellar granule cell precursor proliferation / negative regulation of T cell differentiation in thymus / epithelial cell proliferation involved in salivary gland morphogenesis / epidermal cell fate specification / spinal cord motor neuron differentiation / positive regulation of T cell differentiation in thymus / cell development / mesenchymal cell proliferation involved in lung development / intermediate filament organization / prostate gland development / cerebellar granule cell precursor proliferation / Activation of SMO / embryonic skeletal system development / establishment of epithelial cell polarity / skeletal muscle fiber differentiation / mesenchymal cell apoptotic process / patched binding / negative regulation of cell division / somite development / animal organ formation / embryonic foregut morphogenesis / hindbrain development / neuron fate commitment / ectoderm development / positive regulation of skeletal muscle tissue development / thalamus development / stem cell development / embryonic pattern specification / negative regulation of dopaminergic neuron differentiation / branching involved in salivary gland morphogenesis / skeletal muscle cell proliferation / lymphoid progenitor cell differentiation / positive regulation of immature T cell proliferation in thymus / cellular response to cholesterol / dorsal/ventral neural tube patterning / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / smooth muscle tissue development / negative thymic T cell selection / pattern specification process / artery development / lung-associated mesenchyme development / positive regulation of astrocyte differentiation / oligodendrocyte development / pharyngeal system development / male genitalia development / regulation of stem cell proliferation
Similarity search - Function
Transmembrane receptor, patched / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Protein patched/dispatched / Patched family ...Transmembrane receptor, patched / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Protein patched/dispatched / Patched family / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily
Similarity search - Domain/homology
Protein patched homolog 1 / Sonic hedgehog protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYan N / Gong X
Funding support China, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31621092, 31630017, 31611130036 China
National Basic Research Program of China (973 Program)2015CB910101 China
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.
History
DepositionJun 5, 2018-
Header (metadata) releaseJul 11, 2018-
Map releaseJul 11, 2018-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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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

emd_7968.png

Downloads & links

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Map

FileDownload / File: emd_7968.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.11725369 - 0.21128653
Average (Standard dev.)0.00041769576 (±0.0074620936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 244.38399 Å
α=β=γ: 90.0 °

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
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
Components
  • Organelle or cellular component: Patch1
    • Protein or peptide: Protein patched homolog 1
  • Protein or peptide: Sonic hedgehog protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: SERINE
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION

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Supramolecule #1: Patch1

SupramoleculeName: Patch1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein patched homolog 1

MacromoleculeName: Protein patched homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150.189578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGPDEVDASG RMASAGNAAE PQDRGGGGSG CIGAPGRPAG GGRRRRTGGL RRAAAPDRDY LHRPSYCDAA FALEQISKG KATGRKAPLW LRAKFQRLLF KLGCYIQKNC GKFLVVGLLI FGAFAVGLKA ANLETNVEEL WVEVGGRVSR E LNYTRQKI ...String:
MADYKDDDDK SGPDEVDASG RMASAGNAAE PQDRGGGGSG CIGAPGRPAG GGRRRRTGGL RRAAAPDRDY LHRPSYCDAA FALEQISKG KATGRKAPLW LRAKFQRLLF KLGCYIQKNC GKFLVVGLLI FGAFAVGLKA ANLETNVEEL WVEVGGRVSR E LNYTRQKI GEEAMFNPQL MIQTPKEEGA NVLTTEALLQ HLDSALQASR VHVYMYNRQW KLEHLCYKSG ELITETGYMD QI IEYLYPC LIITPLDCFW EGAKLQSGTA YLLGKPPLRW TNFDPLEFLE ELKKINYQVD SWEEMLNKAE VGHGYMDRPC LNP ADPDCP ATAPNKNSTK PLDMALVLNG GCHGLSRKYM HWQEELIVGG TVKNSTGKLV SAHALQTMFQ LMTPKQMYEH FKGY EYVSH INWNEDKAAA ILEAWQRTYV EVVHQSVAQN STQKVLSFTT TTLDDILKSF SDVSVIRVAS GYLLMLAYAC LTMLR WDCS KSQGAVGLAG VLLVALSVAA GLGLCSLIGI SFNAATTQVL PFLALGVGVD DVFLLAHAFS ETGQNKRIPF EDRTGE CLK RTGASVALTS ISNVTAFFMA ALIPIPALRA FSLQAAVVVV FNFAMVLLIF PAILSMDLYR REDRRLDIFC CFTSPCV SR VIQVEPQAYT DTHDNTRYSP PPPYSSHSFA HETQITMQST VQLRTEYDPH THVYYTTAEP RSEISVQPVT VTQDTLSC Q SPESTSSTRD LLSQFSDSSL HCLEPPCTKW TLSSFAEKHY APFLLKPKAK VVVIFLFLGL LGVSLYGTTR VRDGLDLTD IVPRETREYD FIAAQFKYFS FYNMYIVTQK ADYPNIQHLL YDLHRSFSNV KYVMLEENKQ LPKMWLHYFR DWLQGLQDAF DSDWETGKI MPNNYKNGSD DGVLAYKLLV QTGSRDKPID ISQLTKQRLV DADGIINPSA FYIYLTAWVS NDPVAYAASQ A NIRPHRPE WVHDKADYMP ETRLRIPAAE PIEYAQFPFY LNGLRDTSDF VEAIEKVRTI CSNYTSLGLS SYPNGYPFLF WE QYIGLRH WLLLFISVVL ACTFLVCAVF LLNPWTAGII VMVLALMTVE LFGMMGLIGI KLSAVPVVIL IASVGIGVEF TVH VALAFL TAIGDKNRRA VLALEHMFAP VLDGAVSTLL GVLMLAGSEF DFIVRYFFAV LAILTILGVL NGLVLLPVLL SFFG PYPEV SPANGLNRLP TPSPEPPPSV VRFAMPPGHT HSGSDSSDSE YSSQTTVSGL SEELRHYEAQ QGAGGPAHQV IVEAT ENPV FAHSTVVHPE SRHHPPSNPR QQPHLDSGSL PPGRQGQQPR RDLEGSDEVD AVEGSHHHHH HHHHH

UniProtKB: Protein patched homolog 1

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Macromolecule #2: Sonic hedgehog protein

MacromoleculeName: Sonic hedgehog protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.934461 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
AHMCGPGRGF GKRRHPKKLT PLAYKQFIPN VAEKTLGASG RYEGKISRNS ERFKELTPNY NPDIIFKDEE NTGADRLMTQ RCKDKLNAL AISVMNQWPG VKLRVTEGWD EDGHHSEESL HYEGRAVDIT TSDRDRSKYG MLARLAVEAG FDWVYYESKA H IHCSVKAE NSVAAKSGG

UniProtKB: Sonic hedgehog protein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #6: SERINE

MacromoleculeName: SERINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: SER
Molecular weightTheoretical: 105.093 Da
Chemical component information

ChemComp-SER:
SERINE

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration15 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: RANDOM CONICAL TILT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 137823
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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