+Open data
-Basic information
Entry | Database: PDB / ID: 3u2z | ||||||
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Title | Activator-Bound Structure of Human Pyruvate Kinase M2 | ||||||
Components | Pyruvate kinase isozymes M1/M2 | ||||||
Keywords | transferase/transferase activator / transferase / Structural Genomics / Structural Genomics Consortium / SGC / transferase-transferase activator complex | ||||||
Function / homology | Function and homology information programmed cell death / pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum ...programmed cell death / pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / glycolytic process / non-specific protein-tyrosine kinase / cilium / cellular response to insulin stimulus / extracellular vesicle / MHC class II protein complex binding / protein tyrosine kinase activity / collagen-containing extracellular matrix / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cadherin binding / phosphorylation / mRNA binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å | ||||||
Authors | Hong, B. / Dimov, S. / Tempel, W. / Auld, D. / Thomas, C. / Boxer, M. / Jianq, J.-K. / Skoumbourdis, A. / Min, S. / Southall, N. ...Hong, B. / Dimov, S. / Tempel, W. / Auld, D. / Thomas, C. / Boxer, M. / Jianq, J.-K. / Skoumbourdis, A. / Min, S. / Southall, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Inglese, J. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2012 Title: Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis. Authors: Anastasiou, D. / Yu, Y. / Israelsen, W.J. / Jiang, J.K. / Boxer, M.B. / Hong, B.S. / Tempel, W. / Dimov, S. / Shen, M. / Jha, A. / Yang, H. / Mattaini, K.R. / Metallo, C.M. / Fiske, B.P. / ...Authors: Anastasiou, D. / Yu, Y. / Israelsen, W.J. / Jiang, J.K. / Boxer, M.B. / Hong, B.S. / Tempel, W. / Dimov, S. / Shen, M. / Jha, A. / Yang, H. / Mattaini, K.R. / Metallo, C.M. / Fiske, B.P. / Courtney, K.D. / Malstrom, S. / Khan, T.M. / Kung, C. / Skoumbourdis, A.P. / Veith, H. / Southall, N. / Walsh, M.J. / Brimacombe, K.R. / Leister, W. / Lunt, S.Y. / Johnson, Z.R. / Yen, K.E. / Kunii, K. / Davidson, S.M. / Christofk, H.R. / Austin, C.P. / Inglese, J. / Harris, M.H. / Asara, J.M. / Stephanopoulos, G. / Salituro, F.G. / Jin, S. / Dang, L. / Auld, D.S. / Park, H.W. / Cantley, L.C. / Thomas, C.J. / Vander Heiden, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u2z.cif.gz | 778.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u2z.ent.gz | 646.3 KB | Display | PDB format |
PDBx/mmJSON format | 3u2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/3u2z ftp://data.pdbj.org/pub/pdb/validation_reports/u2/3u2z | HTTPS FTP |
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-Related structure data
Related structure data | 3me3C 3gqyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 3 / Auth seq-ID: 144 - 148 / Label seq-ID: 146 - 150
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Details | The biological unit has not been determined. |
-Components
#1: Protein | Mass: 58160.984 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PKM2, OIP3, PK2, PK3, PKM / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P14618, pyruvate kinase #2: Sugar | ChemComp-FBP / #3: Chemical | ChemComp-UNX / #4: Chemical | #5: 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: 2.4 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 25% PEG-3350, 0.2M ammonium sulfate, 0.1M Bis-Tris. Activator concentration: 0.01M., pH 6.5, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98322 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98322 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 125358 / % possible obs: 98.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.086 / Χ2: 1.815 / Net I/σ(I): 11.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDB entry 3GQY Resolution: 2.1→44.446 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 11.136 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. ACTIVATOR GEOMETRY RESTRAINTS WERE PREPARED BY THE PRODRG SERVER. THE PROGRAM COOT AND THE MOLPROBITY SERVER WERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. ACTIVATOR GEOMETRY RESTRAINTS WERE PREPARED BY THE PRODRG SERVER. THE PROGRAM COOT AND THE MOLPROBITY SERVER WERE ALSO USED DURING REFINEMENT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.51 Å2 / Biso mean: 28.29 Å2 / Biso min: 12.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→44.446 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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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