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Yorodumi- PDB-4c4m: Crystal structure of the Sonic Hedgehog-chondroitin-4-sulphate complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c4m | |||||||||
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Title | Crystal structure of the Sonic Hedgehog-chondroitin-4-sulphate complex | |||||||||
Components | SONIC HEDGEHOG PROTEIN | |||||||||
Keywords | SIGNALING PROTEIN / HEDGEHOG SIGNALLING / MORPHOGENS / HEPARAN SULPHATE PROTEOGLYCANS / GLYCOSAMINOGLYCANS | |||||||||
Function / homology | Function and homology information forebrain regionalization / cell proliferation in external granule layer / zona limitans intrathalamica formation / positive regulation of neurotrophin production / positive regulation of photoreceptor cell differentiation / fungiform papilla development / Release of Hh-Np from the secreting cell / digestive tract mesoderm development / epithelial-mesenchymal signaling involved in prostate gland development / fungiform papilla morphogenesis ...forebrain regionalization / cell proliferation in external granule layer / zona limitans intrathalamica formation / positive regulation of neurotrophin production / positive regulation of photoreceptor cell differentiation / fungiform papilla development / Release of Hh-Np from the secreting cell / digestive tract mesoderm development / epithelial-mesenchymal signaling involved in prostate gland development / fungiform papilla morphogenesis / ventral spinal cord interneuron specification / tongue morphogenesis / respiratory tube development / Ligand-receptor interactions / Activation of SMO / mesenchymal-epithelial cell signaling involved in prostate gland development / positive regulation of oligodendrocyte progenitor proliferation / trachea development / positive regulation of skeletal muscle cell proliferation / anatomical structure formation involved in morphogenesis / 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 / 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 / myotube differentiation / negative regulation of alpha-beta T cell differentiation / regulation of glial cell proliferation / regulation of prostatic bud formation / positive regulation of penile erection / metanephric mesenchymal cell proliferation involved in metanephros development / neural tube formation / formation of anatomical boundary / lung epithelium development / positive regulation of striated muscle cell differentiation / trachea morphogenesis / regulation of epithelial cell proliferation involved in prostate gland development / cholesterol-protein transferase activity / bud outgrowth involved in lung branching / telencephalon regionalization / epithelial-mesenchymal cell signaling / : / laminin-1 binding / vasculogenesis involved in coronary vascular morphogenesis / Hedgehog ligand biogenesis / 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 / 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 / male genitalia morphogenesis / limb bud formation / lung lobe morphogenesis / skeletal muscle fiber differentiation / fungiform papilla formation / thalamus development / embryonic foregut morphogenesis / patched binding / 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 / branching involved in prostate gland morphogenesis / mesenchymal cell proliferation involved in lung development / 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 / mesenchymal cell proliferation Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | |||||||||
Authors | Whalen, D.M. / Malinauskas, T. / Gilbert, R.J.C. / Siebold, C. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structural Insights Into Proteoglycan-Shaped Hedgehog Signaling. Authors: Whalen, D.M. / Malinauskas, T. / Gilbert, R.J.C. / Siebold, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c4m.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c4m.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 4c4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/4c4m ftp://data.pdbj.org/pub/pdb/validation_reports/c4/4c4m | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 18768.016 Da / Num. of mol.: 1 / Fragment: N-TEMINAL SIGNALLING DOMAIN, RESIDUES 40-195 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q62226 |
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#2: Polysaccharide | beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta- ...beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 133 molecules
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | BETA-D-GLUCOPYRANURONIC ACID (BDP): THE OLIGOSACCHARIDE CHAIN BDP-ASG IS CONTINUOUS RUNNING THROUGH ...BETA-D-GLUCOPYRAN |
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Sequence details | CONSTRUCT CONTAINS TWO ADDITIONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.17 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 25% (W/V) PEG 3350, 100 MM HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Date: Jul 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→43.8 Å / Num. obs: 17037 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 17.84 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.74→1.79 Å / Redundancy: 7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→43.828 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 18.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→43.828 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 8.7888 Å / Origin y: -3.2345 Å / Origin z: -13.019 Å
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Refinement TLS group | Selection details: ALL |