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- EMDB-8955: Structure of 2:1 human Ptch1-Shh-N complex -

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Basic information

Entry
Database: EMDB / ID: EMD-8955
TitleStructure of 2:1 human Ptch1-Shh-N complex
Map dataPtch1-Shh-N complex
Sample
  • Complex: Ptc
    • Protein or peptide: Protein patched homolog 1
  • Protein or peptide: Sonic hedgehog protein
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: PALMITIC ACID
Keywordstumor suppressor / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of nodal signaling pathway / positive regulation of skeletal muscle cell proliferation / 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 ...regulation of nodal signaling pathway / positive regulation of skeletal muscle cell proliferation / 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 / neural plate axis specification / regulation of odontogenesis / positive regulation of mesenchymal cell proliferation involved in ureter development / cell differentiation involved in kidney development / trunk neural crest cell migration / Formation of lateral plate mesoderm / hedgehog receptor activity / response to chlorate / neural tube patterning / hindgut morphogenesis / cell proliferation involved in metanephros development / polarity specification of anterior/posterior axis / regulation of glial cell proliferation / negative regulation of alpha-beta T cell differentiation / formation of anatomical boundary / positive regulation of striated muscle cell differentiation / lung epithelium development / metanephric mesenchymal cell proliferation involved in metanephros development / ventral midline development / smoothened binding / trachea morphogenesis / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / bud outgrowth involved in lung branching / hedgehog family protein binding / telencephalon regionalization / epithelial-mesenchymal cell signaling / Ligand-receptor interactions / hindlimb morphogenesis / laminin-1 binding / negative regulation of cholesterol efflux / salivary gland cavitation / spinal cord dorsal/ventral patterning / negative regulation of mesenchymal cell apoptotic process / determination of left/right asymmetry in lateral mesoderm / positive regulation of cerebellar granule cell precursor proliferation / negative regulation of T cell differentiation in thymus / cell development / epidermal cell fate specification / spinal cord motor neuron differentiation / positive regulation of T cell differentiation in thymus / intermediate filament organization / prostate gland development / cerebellar granule cell precursor proliferation / limb bud formation / embryonic skeletal system development / establishment of epithelial cell polarity / skeletal muscle fiber differentiation / limb morphogenesis / lung lobe morphogenesis / Activation of SMO / mesenchymal cell apoptotic process / patched binding / embryonic digestive tract morphogenesis / animal organ formation / negative regulation of cell division / regulation of prostatic bud formation / embryonic foregut morphogenesis / hindbrain development / epithelial cell proliferation involved in salivary gland morphogenesis / ectoderm development / positive regulation of skeletal muscle tissue development / somite development / neuron fate commitment / negative regulation of dopaminergic neuron differentiation / mesenchymal cell proliferation involved in lung development / skeletal muscle cell proliferation / stem cell development / lymphoid progenitor cell differentiation / positive regulation of immature T cell proliferation in thymus / 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 / artery development / thalamus development / cellular response to cholesterol / positive regulation of astrocyte differentiation / pharyngeal system development / self proteolysis / regulation of stem cell proliferation / oligodendrocyte development / mammary gland duct morphogenesis / mammary gland epithelial cell differentiation / positive regulation of epithelial cell proliferation involved in prostate gland development / male genitalia 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 SSD ...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 SSD / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / 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 / Resolution: 3.5 Å
AuthorsQi X / Li X / Wang J
CitationJournal: Science / Year: 2018
Title: Two Patched molecules engage distinct sites on Hedgehog yielding a signaling-competent complex.
Authors: Xiaofeng Qi / Philip Schmiege / Elias Coutavas / Xiaochun Li /
Abstract: Aberrant Hedgehog (HH) signaling leads to various types of cancer and birth defects. N-terminally palmitoylated HH initiates signaling by binding its receptor Patched-1 (PTCH1). A recent 1:1 PTCH1-HH ...Aberrant Hedgehog (HH) signaling leads to various types of cancer and birth defects. N-terminally palmitoylated HH initiates signaling by binding its receptor Patched-1 (PTCH1). A recent 1:1 PTCH1-HH complex structure visualized a palmitate-mediated binding site on HH, which was inconsistent with previous studies that implied a distinct, calcium-mediated binding site for PTCH1 and HH co-receptors. Our 3.5-angstrom resolution cryo-electron microscopy structure of native Sonic Hedgehog (SHH-N) in complex with PTCH1 at a physiological calcium concentration reconciles these disparate findings and demonstrates that one SHH-N molecule engages both epitopes to bind two PTCH1 receptors in an asymmetric manner. Functional assays using PTCH1 or SHH-N mutants that disrupt the individual interfaces illustrate that simultaneous engagement of both interfaces is required for efficient signaling in cells.
History
Header (metadata) releaseMay 16, 2018-
DepositionJul 9, 2018-
Map releaseAug 29, 2018-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6e1h
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rvd
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8955.png

Downloads & links

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Map

FileDownload / File: emd_8955.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPtch1-Shh-N complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 280 pix.
= 280. Å		1 Å/pix.
x 280 pix.
= 280. Å		1 Å/pix.
x 280 pix.
= 280. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.436 / Movie #1: 0.5
Minimum - Maximum-1.0071659 - 2.2087946
Average (Standard dev.)0.0049828757 (±0.08871832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 280.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z280.000280.000280.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-1.0072.2090.005

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Supplemental data

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Sample components

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Entire : Ptc

EntireName: Ptc
Components
  • Complex: Ptc
    • Protein or peptide: Protein patched homolog 1
  • Protein or peptide: Sonic hedgehog protein
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: PALMITIC ACID

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Supramolecule #1: Ptc

SupramoleculeName: Ptc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 265 KDa

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Macromolecule #1: Protein patched homolog 1

MacromoleculeName: Protein patched homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 160.714406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASAGNAAEP QDRGGGGSGC IGAPGRPAGG GRRRRTGGLR RAAAPDRDYL HRPSYCDAAF ALEQISKGKA TGRKAPLWLR AKFQRLLFK LGCYIQKNCG KFLVVGLLIF GAFAVGLKAA NLETNVEELW VEVGGRVSRE LNYTRQKIGE EAMFNPQLMI Q TPKEEGAN ...String:
MASAGNAAEP QDRGGGGSGC IGAPGRPAGG GRRRRTGGLR RAAAPDRDYL HRPSYCDAAF ALEQISKGKA TGRKAPLWLR AKFQRLLFK LGCYIQKNCG KFLVVGLLIF GAFAVGLKAA NLETNVEELW VEVGGRVSRE LNYTRQKIGE EAMFNPQLMI Q TPKEEGAN VLTTEALLQH LDSALQASRV HVYMYNRQWK LEHLCYKSGE LITETGYMDQ IIEYLYPCLI ITPLDCFWEG AK LQSGTAY LLGKPPLRWT NFDPLEFLEE LKKINYQVDS WEEMLNKAEV GHGYMDRPCL NPADPDCPAT APNKNSTKPL DMA LVLNGG CHGLSRKYMH WQEELIVGGT VKNSTGKLVS AHALQTMFQL MTPKQMYEHF KGYEYVSHIN WNEDKAAAIL EAWQ RTYVE VVHQSVAQNS TQKVLSFTTT TLDDILKSFS DVSVIRVASG YLLMLAYACL TMLRWDCSKS QGAVGLAGVL LVALS VAAG LGLCSLIGIS FNAATTQVLP FLALGVGVDD VFLLAHAFSE TGQNKRIPFE DRTGECLKRT GASVALTSIS NVTAFF MAA LIPIPALRAF SLQAAVVVVF NFAMVLLIFP AILSMDLYRR EDRRLDIFCC FTSPCVSRVI QVEPQAYTDT HDNTRYS PP PPYSSHSFAH ETQITMQSTV QLRTEYDPHT HVYYTTAEPR SEISVQPVTV TQDTLSCQSP ESTSSTRDLL SQFSDSSL H CLEPPCTKWT LSSFAEKHYA PFLLKPKAKV VVIFLFLGLL GVSLYGTTRV RDGLDLTDIV PRETREYDFI AAQFKYFSF YNMYIVTQKA DYPNIQHLLY DLHRSFSNVK YVMLEENKQL PKMWLHYFRD WLQGLQDAFD SDWETGKIMP NNYKNGSDDG VLAYKLLVQ TGSRDKPIDI SQLTKQRLVD ADGIINPSAF YIYLTAWVSN DPVAYAASQA NIRPHRPEWV HDKADYMPET R LRIPAAEP IEYAQFPFYL NGLRDTSDFV EAIEKVRTIC SNYTSLGLSS YPNGYPFLFW EQYIGLRHWL LLFISVVLAC TF LVCAVFL LNPWTAGIIV MVLALMTVEL FGMMGLIGIK LSAVPVVILI ASVGIGVEFT VHVALAFLTA IGDKNRRAVL ALE HMFAPV LDGAVSTLLG VLMLAGSEFD FIVRYFFAVL AILTILGVLN GLVLLPVLLS FFGPYPEVSP ANGLNRLPTP SPEP PPSVV RFAMPPGHTH SGSDSSDSEY SSQTTVSGLS EELRHYEAQQ GAGGPAHQVI VEATENPVFA HSTVVHPESR HHPPS NPRQ QPHLDSGSLP PGRQGQQPRR DPPREGLWPP PYRPRRDAFE ISTEGHSGPS NRARWGPRGA RSHNPRNPAS TAMGSS VPG YCQPITTVTA SASVTVAVHP PPVPGPGRNP RGGLCPGYPE TDHGLFEDPH VPFHVRCERR DSKVEVIELQ DVECEER PR GSSSN

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: 19.594039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CGPGRGFGKR RHPKKLTPLA YKQFIPNVAE KTLGASGRYE GKISRNSERF KELTPNYNPD IIFKDEENTG ADRLMTQRCK DKLNALAIS VMNQWPGVKL RVTEGWDEDG HHSEESLHYE GRAVDITTSD RDRSKYGMLA RLAVEAGFDW VYYESKAHIH C SVKAENSV AAKSGG

UniProtKB: Sonic hedgehog protein

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5u73

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77712
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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