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Yorodumi- PDB-3ho5: Crystal structure of Hedgehog-interacting protein (HHIP) and Soni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ho5 | ||||||
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Title | Crystal structure of Hedgehog-interacting protein (HHIP) and Sonic hedgehog (SHH) complex | ||||||
Components |
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Keywords | 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 | Function and homology information regulation of fibroblast growth factor receptor 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 fibroblast growth factor receptor 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 / regulation of odontogenesis / positive regulation of mesenchymal cell proliferation involved in ureter development / polarity specification of anterior/posterior axis / trunk neural crest cell migration / Formation of lateral plate mesoderm / 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 / negative regulation of cholesterol efflux / salivary gland cavitation / spinal cord dorsal/ventral patterning / determination of left/right asymmetry in lateral mesoderm / 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 / cerebellar granule cell precursor proliferation / intermediate filament organization / mesenchymal cell apoptotic process / prostate gland development / embryonic skeletal system development / limb bud formation / lung lobe morphogenesis / Activation of SMO / establishment of epithelial cell polarity / skeletal muscle fiber differentiation / thalamus development / embryonic digestive tract morphogenesis / somite development / patched binding / embryonic foregut morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / hindbrain development / animal organ formation / ectoderm development / positive regulation of skeletal muscle tissue development / neuron fate commitment / stem cell development / negative regulation of dopaminergic neuron differentiation / mesenchymal cell proliferation involved in lung development / skeletal muscle cell proliferation / negative thymic T cell selection / 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 / 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 / lung-associated mesenchyme development / Formation of axial mesoderm / regulation of proteolysis / dopaminergic neuron differentiation / intein-mediated protein splicing / positive thymic T cell selection / metanephros development / metanephric collecting duct development / glycosaminoglycan binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Hymowitz, S.G. / Bosanac, I. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ho5.cif.gz | 218.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ho5.ent.gz | 173.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ho5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ho5_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 3ho5_full_validation.pdf.gz | 481.4 KB | Display | |
Data in XML | 3ho5_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 3ho5_validation.cif.gz | 52.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/3ho5 ftp://data.pdbj.org/pub/pdb/validation_reports/ho/3ho5 | HTTPS FTP |
-Related structure data
Related structure data | 3ho3C 3ho4SC 1vhhS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Homo sapiens (human) / Gene: HHIP, HIP, UNQ5825/PRO19644 Plasmid: pENTR/D-TOPO with honeybee melittin secretion signal Cell line (production host): insect cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96QV1 #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.) Homo sapiens (human) / Gene: SHH / Plasmid: pET101/D-TOPO (Invitrogen) / Cell line (production host): Rosetta 2 (Novagen) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15465 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97839 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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