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- PDB-3ho5: Crystal structure of Hedgehog-interacting protein (HHIP) and Soni... -
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Basic information
Entry | Database: PDB / ID: 3ho5 | ||||||
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Title | Crystal structure of Hedgehog-interacting protein (HHIP) and Sonic hedgehog (SHH) complex | ||||||
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![]() | SIGNALING PROTEIN / receptor ectodomain / six-bladed-propeller domain / EGF domain / disulfide bond / calcium cation / zinc cation / Cell membrane / EGF-like domain / Glycoprotein / Membrane / Secreted / Autocatalytic cleavage / Developmental protein / Disease mutation / Holoprosencephaly / Hydrolase / Lipoprotein / Microphthalmia / Palmitate / Protease | ||||||
Function / homology | ![]() regulation of fibroblast growth factor receptor signaling pathway / Formation of lateral plate mesoderm / 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 ...regulation of fibroblast growth factor receptor signaling pathway / Formation of lateral plate mesoderm / 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 / regulation of odontogenesis / positive regulation of mesenchymal cell proliferation involved in ureter development / polarity specification of anterior/posterior axis / trunk neural crest cell migration / 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 / 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 / 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 / cell development / positive regulation of cerebellar granule cell precursor proliferation / negative regulation of T cell differentiation in thymus / 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 / limb bud formation / lung lobe morphogenesis / prostate gland development / Activation of SMO / skeletal muscle fiber differentiation / establishment of epithelial cell polarity / thalamus development / embryonic digestive tract morphogenesis / embryonic foregut morphogenesis / somite development / patched binding / epithelial cell proliferation involved in salivary gland morphogenesis / hindbrain development / positive regulation of skeletal muscle tissue development / animal organ formation / ectoderm development / neuron fate commitment / stem cell development / dorsal/ventral neural tube patterning / negative regulation of dopaminergic neuron differentiation / mesenchymal cell proliferation involved in lung development / negative thymic T cell selection / skeletal muscle cell proliferation / lymphoid progenitor cell differentiation / positive regulation of immature T cell proliferation in thymus / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / smooth muscle tissue development / regulation of stem cell proliferation / oligodendrocyte development / male genitalia development / artery development / positive regulation of astrocyte differentiation / pattern specification process / self proteolysis / epithelial cell proliferation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / embryonic pattern specification / branching involved in salivary gland morphogenesis / Release of Hh-Np from the secreting cell / Formation of axial mesoderm / lung-associated mesenchyme development / dopaminergic neuron differentiation / regulation of proteolysis / metanephros development / positive thymic T cell selection / intein-mediated protein splicing / glycosaminoglycan binding / metanephric collecting duct development Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hymowitz, S.G. / Bosanac, I. | ||||||
![]() | ![]() Title: The structure of SHH in complex with HHIP reveals a recognition role for the Shh pseudo active site in signaling. Authors: Bosanac, I. / Maun, H.R. / Scales, S.J. / Wen, X. / Lingel, A. / Bazan, J.F. / de Sauvage, F.J. / Hymowitz, S.G. / Lazarus, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.5 KB | Display | ![]() |
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PDB format | ![]() | 173.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 453.3 KB | Display | ![]() |
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Full document | ![]() | 481.4 KB | Display | |
Data in XML | ![]() | 38.8 KB | Display | |
Data in CIF | ![]() | 52.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ho3C ![]() 3ho4SC ![]() 1vhhS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 54087.246 Da / Num. of mol.: 2 / Fragment: UNP residues 193-667 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pENTR/D-TOPO with honeybee melittin secretion signal Cell line (production host): insect cells / Production host: ![]() #2: Protein | | Mass: 19122.484 Da / Num. of mol.: 1 / Fragment: UNP residues 29-197 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | Compound details | THE SECOND MOLECULE OF SONIC HEDGEHOG PROTEIN WAS CRYSTALLIZED BUT APPEARED TO BE LARGELY ...THE SECOND MOLECULE OF SONIC HEDGEHOG PROTEIN WAS CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.31 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M bis-Tris propane pH 7.0 and 2.2-2.5 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 6, 2007 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97839 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 37181 / Num. obs: 37106 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rsym value: 0.085 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.589 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 1VHH, 3HO4 Resolution: 3.01→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.885 / SU B: 40.143 / SU ML: 0.336 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.342 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96.674 Å2
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Refinement step | Cycle: LAST / Resolution: 3.01→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.005→3.066 Å / Total num. of bins used: 25
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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