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- PDB-1fmo: CRYSTAL STRUCTURE OF A POLYHISTIDINE-TAGGED RECOMBINANT CATALYTIC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fmo | ||||||
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Title | CRYSTAL STRUCTURE OF A POLYHISTIDINE-TAGGED RECOMBINANT CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE COMPLEXED WITH THE PEPTIDE INHIBITOR PKI(5-24) AND ADENOSINE | ||||||
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![]() | COMPLEX (PHOSPHOTRANSFERASE/INHIBITOR) / COMPLEX (PHOSPHOTRANSFERASE-INHIBITOR) / PHOSPHORYLATION / POLYHISTIDINE-TAG / PROTEIN KINASE / COMPLEX (PHOSPHOTRANSFERASE-INHIBITOR) complex | ||||||
Function / homology | ![]() spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / negative regulation of cAMP-dependent protein kinase activity / Factors involved in megakaryocyte development and platelet production / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / Mitochondrial protein degradation / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / regulation of cellular respiration / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / molecular function inhibitor activity / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / sperm midpiece / negative regulation of TORC1 signaling / regulation of synaptic transmission, glutamatergic / regulation of G2/M transition of mitotic cell cycle / protein kinase A signaling / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / modulation of chemical synaptic transmission / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / small GTPase binding / mRNA processing / presynapse / manganese ion binding / cellular response to heat / peptidyl-serine phosphorylation / postsynapse / dendritic spine / molecular adaptor activity / regulation of cell cycle / protein kinase activity / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / mitochondrion / nucleoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Narayana, N. / Cox, S. / Shaltiel, S. / Taylor, S.S. / Xuong, N.-H. | ||||||
![]() | ![]() Title: Crystal structure of a polyhistidine-tagged recombinant catalytic subunit of cAMP-dependent protein kinase complexed with the peptide inhibitor PKI(5-24) and adenosine. Authors: Narayana, N. / Cox, S. / Shaltiel, S. / Taylor, S.S. / Xuong, N. #1: ![]() Title: A Binary Complex of the Catalytic Subunit of Camp-Dependent Protein Kinase and Adenosine Further Defines Conformational Flexibility Authors: Narayana, N. / Cox, S. / Xuong, N.H. / Ten Eyck, L.F. / Taylor, S.S. #2: ![]() Title: Crystal Structure of the Catalytic Subunit of Camp-Dependent Protein Kinase Complexed with Mgatp and Peptide Inhibitor Authors: Zheng, J. / Knighton, D.R. / Ten Eyck, L.F. / Karlsson, R. / Xuong, N.H. / Taylor, S.S. / Sowadski, J.M. #3: ![]() Title: Expression of the Catalytic Subunit of Camp-Dependent Protein Kinase in Escherichia Coli: Multiple Isozymes Reflect Different Phosphorylation States Authors: Herberg, F.W. / Bell, S.M. / Taylor, S.S. #4: ![]() Title: Crystal Structure of the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase Authors: Knighton, D.R. / Zheng, J.H. / Ten Eyck, L.F. / Ashford, V.A. / Xuong, N.H. / Taylor, S.S. / Sowadski, J.M. #5: ![]() Title: Structure of a Peptide Inhibitor Bound to the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase Authors: Knighton, D.R. / Zheng, J.H. / Ten Eyck, L.F. / Xuong, N.H. / Taylor, S.S. / Sowadski, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.9 KB | Display | ![]() |
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PDB format | ![]() | 67 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1apmS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40657.316 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 5 - 24 Source method: isolated from a genetically manipulated source References: UniProt: P61926 |
#3: Chemical | ChemComp-ADN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ORTHORHOMBIC CRYSTALS OF THE TERNARY COMPLEX, COMPRISED OF MOUSE HIS6-RC SUBUNIT, PKI (5-24) AND ADENOSINE, WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD USING 2-METHYL-2,4- ...Details: ORTHORHOMBIC CRYSTALS OF THE TERNARY COMPLEX, COMPRISED OF MOUSE HIS6-RC SUBUNIT, PKI (5-24) AND ADENOSINE, WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD USING 2-METHYL-2,4-PENTANEDIOL (MPD) AS THE PRECIPITATING AGENT. THE MOTHER-LIQUOR CONTAINED PROTEIN AT A CONCENTRATION OF 0.25 MM IN 100 MM BICINE BUFFER AT PH 8.0, 0.75 MM PKI(5-24), 4 MM ADENOSINE AND 4% MPD. THE RESERVOIR SOLUTION WAS MADE UP OF 20% MPD IN 100 MM BICINE BUFFER (PH 8.0). X-RAY DIFFRACTION QUALITY CRYSTALS (0.2 X 0.15 X 0.8 MM3) WERE GROWN AT 4 C IN APPROXIMATELY 4 - 6 WEEKS., vapor diffusion - hanging drop, temperature 277K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Feb 7, 1994 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 21679 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.064 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1 / Rsym value: 0.25 / % possible all: 84 |
Reflection | *PLUS Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 84 % / Rmerge(I) obs: 0.25 |
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Processing
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Refinement | Method to determine structure: ISOMORPHOUS REPLACEMENT Starting model: PDB ENTRY 1APM Resolution: 2.2→10 Å / σ(F): 1
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Solvent computation | Bsol: 167.1 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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