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Yorodumi- PDB-5mgx: The structure of FKBP38 in complex with the MEEVD tetratricopepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mgx | ||||||
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Title | The structure of FKBP38 in complex with the MEEVD tetratricopeptide binding-motif of Hsp90 | ||||||
Components |
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Keywords | ISOMERASE / Hsp90 / PPIase / teratricopeptide / immunophilin | ||||||
Function / homology | Function and homology information The NLRP3 inflammasome / neuron fate specification / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation ...The NLRP3 inflammasome / neuron fate specification / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / dorsal/ventral neural tube patterning / regulation of autophagy of mitochondrion / : / protein localization to mitochondrion / protein targeting to mitochondrion / positive regulation of BMP signaling pathway / mitochondrial envelope / camera-type eye development / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / smoothened signaling pathway / protein maturation / proteasome assembly / endomembrane system / BMP signaling pathway / protein folding chaperone / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mitochondrial membrane / ATP-dependent protein folding chaperone / multicellular organism growth / disordered domain specific binding / unfolded protein binding / protein folding / cellular response to heat / protein refolding / regulation of gene expression / protein stabilization / calmodulin binding / Ub-specific processing proteases / intracellular signal transduction / apoptotic process / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Roe, S.M. / Blundell, K.L. / Prodromou, C. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: PLoS ONE / Year: 2017 Title: The structure of FKBP38 in complex with the MEEVD tetratricopeptide binding-motif of Hsp90. Authors: Blundell, K.L. / Pal, M. / Roe, S.M. / Pearl, L.H. / Prodromou, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mgx.cif.gz | 238.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mgx.ent.gz | 188.9 KB | Display | PDB format |
PDBx/mmJSON format | 5mgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/5mgx ftp://data.pdbj.org/pub/pdb/validation_reports/mg/5mgx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 966.963 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02829*PLUS #2: Protein | Mass: 31804.686 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP8, FKBP38 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14318, peptidylprolyl isomerase #3: Water | ChemComp-HOH / | |
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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: 2.99 Å3/Da / Density % sol: 58.93 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop Details: 0.02 M sodium potassium phosphate, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→100 Å / Num. obs: 76276 / % possible obs: 95.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 23.1 Å2 / CC1/2: 0.947 / Rmerge(I) obs: 0.111 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.18→2.24 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.733 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AWG and 2FBN Resolution: 2.18→100 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.814 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.284 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.237
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Displacement parameters | Biso mean: 33.57 Å2
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Refine analyze | Luzzati coordinate error obs: 0.41 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.18→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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