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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 IONCalcium
Function / homology
Function and homology information


Formation of lateral plate mesoderm / 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 ...Formation of lateral plate mesoderm / 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 / polarity specification of anterior/posterior axis / trunk neural crest cell migration / hedgehog receptor activity / response to chlorate / cell proliferation involved in metanephros development / hindgut morphogenesis / 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 / neural tube patterning / 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 / : / laminin-1 binding / Ligand-receptor interactions / hindlimb morphogenesis / salivary gland cavitation / negative regulation of cholesterol efflux / determination of left/right asymmetry in lateral mesoderm / spinal cord dorsal/ventral patterning / negative regulation of mesenchymal cell apoptotic process / positive regulation of cerebellar granule cell precursor proliferation / cell development / negative regulation of T cell differentiation in thymus / epidermal cell fate specification / spinal cord motor neuron differentiation / positive regulation of T cell differentiation in thymus / intermediate filament organization / cerebellar granule cell precursor proliferation / mesenchymal cell apoptotic process / embryonic skeletal system development / prostate gland development / establishment of epithelial cell polarity / limb bud formation / lung lobe morphogenesis / Activation of SMO / negative regulation of cell division / skeletal muscle fiber differentiation / thalamus development / embryonic foregut morphogenesis / patched binding / limb morphogenesis / embryonic digestive tract morphogenesis / somite development / hindbrain development / negative thymic T cell selection / positive regulation of skeletal muscle tissue development / ectoderm development / epithelial cell proliferation involved in salivary gland morphogenesis / animal organ formation / neuron fate commitment / dorsal/ventral neural tube patterning / stem cell development / mesenchymal cell proliferation involved in lung development / cellular response to cholesterol / negative regulation of dopaminergic neuron differentiation / skeletal muscle cell proliferation / positive regulation of immature T cell proliferation in thymus / oligodendrocyte development / lymphoid progenitor cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / smooth muscle tissue development / male genitalia development / positive regulation of astrocyte differentiation / regulation of stem cell proliferation / pattern specification process / artery development / self proteolysis / epithelial cell proliferation involved in prostate gland development / pharyngeal system development
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 / Sterol-sensing domain (SSD) profile. ...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 / Qian HW
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-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing 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)
Voxel sizeX=Y=Z: 1.091 Å
Density
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 IONCalcium

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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)
Recombinant expressionOrganism: 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

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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

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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 / N-Acetylglucosamine

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

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 137823

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