+Open data
-Basic information
Entry | Database: PDB / ID: 6lph | ||||||
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Title | the Sufu-Fu complex crystal structure | ||||||
Components |
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Keywords | PROTEIN BINDING / kinases / phosphorylation | ||||||
Function / homology | Function and homology information : / Hedgehog signaling complex / Assembly of the CI containing complexes / negative regulation of nucleocytoplasmic transport / Activation of CI / Activation of SMO / Hedgehog 'off' state / Phosphorylation of CI / germarium-derived egg chamber formation / Phosphorylation of SMO ...: / Hedgehog signaling complex / Assembly of the CI containing complexes / negative regulation of nucleocytoplasmic transport / Activation of CI / Activation of SMO / Hedgehog 'off' state / Phosphorylation of CI / germarium-derived egg chamber formation / Phosphorylation of SMO / Assembly of the 'signalling complexes' / Ubiquitination and proteolysis of phosphorylated CI / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / wing disc pattern formation / positive regulation of nucleocytoplasmic transport / Hedgehog 'on' state / smoothened binding / segment polarity determination / protein serine/threonine kinase activity => GO:0004674 / intraciliary transport / cytoplasmic sequestering of protein / molecular sequestering activity / negative regulation of BMP signaling pathway / nuclear localization sequence binding / smoothened signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / transcription factor binding / negative regulation of smoothened signaling pathway / positive regulation of protein ubiquitination / cilium / DNA-binding transcription factor binding / protein autophosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / protein-containing complex / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Hua, L. / Geng, W. | ||||||
Citation | Journal: To Be Published Title: Structure of the Sufu-Fu complex at 1.9 Angstroms resolution. Authors: Hua, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lph.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lph.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lph_validation.pdf.gz | 437.6 KB | Display | wwPDB validaton report |
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Full document | 6lph_full_validation.pdf.gz | 446.1 KB | Display | |
Data in XML | 6lph_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 6lph_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/6lph ftp://data.pdbj.org/pub/pdb/validation_reports/lp/6lph | HTTPS FTP |
-Related structure data
Related structure data | 4kmdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29311.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Su(fu) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VG38 |
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#2: Protein/peptide | Mass: 3021.368 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: fu / Production host: Escherichia coli (E. coli) References: UniProt: P23647, non-specific serine/threonine protein kinase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.56 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1% w/v Tryptone, 0.05M HEPES sodium pH7.0, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.91878 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91878 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→55.67 Å / Num. obs: 20919 / % possible obs: 99.7 % / Redundancy: 7.5 % / CC1/2: 0.893 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.91→1.98 Å / Rmerge(I) obs: 0.639 / Num. unique obs: 20919 / CC1/2: 0.893 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KMD Resolution: 1.91→55.67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.234 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.148 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.07 Å2 / Biso mean: 24.615 Å2 / Biso min: 8.72 Å2
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Refinement step | Cycle: final / Resolution: 1.91→55.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.913→1.963 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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