[English] 日本語
Yorodumi- PDB-3te5: structure of the regulatory fragment of sacchromyces cerevisiae a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3te5 | ||||||
---|---|---|---|---|---|---|---|
Title | structure of the regulatory fragment of sacchromyces cerevisiae ampk in complex with NADH | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / CBS domain / Nucleotide binding / cytosol | ||||||
Function / homology | Function and homology information fungal-type cell wall assembly / positive regulation of pseudohyphal growth / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / single-species surface biofilm formation / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine metabolism ...fungal-type cell wall assembly / positive regulation of pseudohyphal growth / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / single-species surface biofilm formation / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine metabolism / invasive growth in response to glucose limitation / peroxisome organization / Macroautophagy / filamentous growth / nucleotide-activated protein kinase complex / protein kinase regulator activity / enzyme-substrate adaptor activity / vacuolar membrane / AMP-activated protein kinase activity / nuclear envelope lumen / AMP binding / establishment of mitotic spindle orientation / positive regulation of macroautophagy / response to unfolded protein / regulation of protein-containing complex assembly / cellular response to glucose starvation / positive regulation of gluconeogenesis / response to endoplasmic reticulum stress / protein serine/threonine kinase activator activity / guanyl-nucleotide exchange factor activity / molecular function activator activity / autophagy / nuclear membrane / negative regulation of translation / carbohydrate metabolic process / non-specific serine/threonine protein kinase / intracellular signal transduction / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / protein kinase binding / signal transduction / mitochondrion / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Mayer, F.V. / Heath, R. / Underwood, E. / Sanders, M.J. / Carmena, D. / McCartney, R. / Leiper, F.C. / Xiao, B. / Jing, C. / Walker, P.A. ...Mayer, F.V. / Heath, R. / Underwood, E. / Sanders, M.J. / Carmena, D. / McCartney, R. / Leiper, F.C. / Xiao, B. / Jing, C. / Walker, P.A. / Haire, L.F. / Ogrodowicz, R. / Martin, S.R. / Schmidt, M.C. / Gamblin, S.J. / Carling, D. | ||||||
Citation | Journal: Cell Metab / Year: 2011 Title: ADP Regulates SNF1, the Saccharomyces cerevisiae Homolog of AMP-Activated Protein Kinase. Authors: Mayer, F.V. / Heath, R. / Underwood, E. / Sanders, M.J. / Carmena, D. / McCartney, R.R. / Leiper, F.C. / Xiao, B. / Jing, C. / Walker, P.A. / Haire, L.F. / Ogrodowicz, R. / Martin, S.R. / ...Authors: Mayer, F.V. / Heath, R. / Underwood, E. / Sanders, M.J. / Carmena, D. / McCartney, R.R. / Leiper, F.C. / Xiao, B. / Jing, C. / Walker, P.A. / Haire, L.F. / Ogrodowicz, R. / Martin, S.R. / Schmidt, M.C. / Gamblin, S.J. / Carling, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3te5.cif.gz | 127.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3te5.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 3te5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/3te5 ftp://data.pdbj.org/pub/pdb/validation_reports/te/3te5 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20454.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SNF1, CAT1, CCR1, GLC2, PAS14, YDR477W, D8035.20 / Production host: Escherichia coli (E. coli) References: UniProt: P06782, non-specific serine/threonine protein kinase |
---|---|
#2: Protein | Mass: 13036.580 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SIP2, SPM2, YGL208W, G1155 / Production host: Escherichia coli (E. coli) / References: UniProt: P34164 |
#3: Protein | Mass: 36512.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SNF4, CAT3, YGL115W / Production host: Escherichia coli (E. coli) / References: UniProt: P12904 |
#4: Chemical | ChemComp-NAI / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.17 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1M Succinic Acid, 0.1M Hepes, 1% w/v Polyethylene glycol monomethyl ether 2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2010 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 30340 / Num. obs: 30327 / % possible obs: 99.84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.088 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.014 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.635 Å / Total num. of bins used: 10
|