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Yorodumi- PDB-2uv4: Crystal Structure of a CBS domain pair from the regulatory gamma1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uv4 | ||||||
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Title | Crystal Structure of a CBS domain pair from the regulatory gamma1 subunit of human AMPK in complex with AMP | ||||||
Components | 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1 | ||||||
Keywords | TRANSFERASE / CBS DOMAIN / LIPID SYNTHESIS / FATTY ACID BIOSYNTHESIS / AMPK GAMMA1 SUBUNIT CBS 3 PLUS 4 AMP REGULATORY SUBUNIT | ||||||
Function / homology | Function and homology information Lipophagy / import into nucleus / cAMP-dependent protein kinase regulator activity / protein kinase regulator activity / Energy dependent regulation of mTOR by LKB1-AMPK / nucleotide-activated protein kinase complex / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of glycolytic process / cAMP-dependent protein kinase activity / Macroautophagy ...Lipophagy / import into nucleus / cAMP-dependent protein kinase regulator activity / protein kinase regulator activity / Energy dependent regulation of mTOR by LKB1-AMPK / nucleotide-activated protein kinase complex / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of glycolytic process / cAMP-dependent protein kinase activity / Macroautophagy / AMP binding / cellular response to nutrient levels / positive regulation of protein kinase activity / Activation of AMPK downstream of NMDARs / Translocation of SLC2A4 (GLUT4) to the plasma membrane / ADP binding / TP53 Regulates Metabolic Genes / fatty acid biosynthetic process / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / protein kinase activity / protein phosphorylation / positive regulation of gene expression / protein kinase binding / signal transduction / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.33 Å | ||||||
Authors | Day, P. / Sharff, A. / PArra, L. / Cleasby, A. / Williams, M. / Horer, S. / Nar, H. / Redemann, N. / Tickle, I. / Yon, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Structure of a Cbs-Domain Pair from the Regulatory Gamma1 Subunit of Human Ampk in Complex with AMP and Zmp. Authors: Day, P. / Sharff, A. / Parra, L. / Cleasby, A. / Williams, M. / Horer, S. / Nar, H. / Redemann, N. / Tickle, I. / Yon, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uv4.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uv4.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 2uv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/2uv4 ftp://data.pdbj.org/pub/pdb/validation_reports/uv/2uv4 | 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
#1: Protein | Mass: 17278.875 Da / Num. of mol.: 1 / Fragment: CBS 3 AND 4 FRAGMENT, RESIDUES 182-325 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54619 |
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#2: Chemical | ChemComp-AMP / |
#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: 1.78 Å3/Da / Density % sol: 30.33 % |
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Crystal grow | pH: 8 / Details: pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 23, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→34.92 Å / Num. obs: 31832 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.18 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.33→1.38 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.1 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.33→34.92 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.938 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.75 Å2
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Refinement step | Cycle: LAST / Resolution: 1.33→34.92 Å
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Refine LS restraints |
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