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- PDB-8gmb: Crystal structure of the full-length Bruton's tyrosine kinase (PH... -
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Basic information
Entry | Database: PDB / ID: 8gmb | ||||||
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Title | Crystal structure of the full-length Bruton's tyrosine kinase (PH-TH domain not visible) | ||||||
![]() | Tyrosine-protein kinase BTK | ||||||
![]() | TRANSFERASE / ATP-binding / Lipid-binding / transcription regulation / immunity | ||||||
Function / homology | ![]() negative regulation of B cell activation / G beta:gamma signalling through BTK / RHO GTPases Activate WASPs and WAVEs / FCERI mediated Ca+2 mobilization / G alpha (q) signalling events / G alpha (12/13) signalling events / negative regulation of leukocyte proliferation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of actin dynamics for phagocytic cup formation / proteoglycan catabolic process ...negative regulation of B cell activation / G beta:gamma signalling through BTK / RHO GTPases Activate WASPs and WAVEs / FCERI mediated Ca+2 mobilization / G alpha (q) signalling events / G alpha (12/13) signalling events / negative regulation of leukocyte proliferation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of actin dynamics for phagocytic cup formation / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / eosinophil homeostasis / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell / neutrophil homeostasis / cellular response to molecule of fungal origin / positive regulation of type I hypersensitivity / cellular response to interleukin-7 / DAP12 signaling / negative regulation of cytokine production / positive regulation of immunoglobulin production / positive regulation of NLRP3 inflammasome complex assembly / phospholipase activator activity / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / positive regulation of B cell proliferation / positive regulation of phagocytosis / cell maturation / : / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cellular response to reactive oxygen species / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / T cell receptor signaling pathway / cytoplasmic vesicle / protein tyrosine kinase activity / adaptive immune response / response to lipopolysaccharide / intracellular signal transduction / membrane raft / phosphorylation / innate immune response / apoptotic process / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
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![]() | Lin, D.Y. / Andreotti, A.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states. Authors: David Yin-Wei Lin / Lauren E Kueffer / Puneet Juneja / Thomas E Wales / John R Engen / Amy H Andreotti / ![]() Abstract: Full-length Bruton's tyrosine kinase (BTK) has been refractory to structural analysis. The nearest full-length structure of BTK to date consists of the autoinhibited SH3-SH2-kinase core. Precisely ...Full-length Bruton's tyrosine kinase (BTK) has been refractory to structural analysis. The nearest full-length structure of BTK to date consists of the autoinhibited SH3-SH2-kinase core. Precisely how the BTK N-terminal domains (the Pleckstrin homology/Tec homology [PHTH] domain and proline-rich regions [PRR] contain linker) contribute to BTK regulation remains unclear. We have produced crystals of full-length BTK for the first time but despite efforts to stabilize the autoinhibited state, the diffraction data still reveal only the SH3-SH2-kinase core with no electron density visible for the PHTH-PRR segment. Cryo-electron microscopy (cryoEM) data of full-length BTK, on the other hand, provide the first view of the PHTH domain within full-length BTK. CryoEM reconstructions support conformational heterogeneity in the PHTH-PRR region wherein the globular PHTH domain adopts a range of states arrayed around the autoinhibited SH3-SH2-kinase core. On the way to activation, disassembly of the SH3-SH2-kinase core opens a new autoinhibitory site on the kinase domain for PHTH domain binding that is ultimately released upon interaction of PHTH with phosphatidylinositol (3,4,5)-trisphosphate. Membrane-induced dimerization activates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to trans-autophosphorylation. Together, these data provide the first structural elucidation of full-length BTK and allow a deeper understanding of allosteric control over the BTK kinase domain during distinct stages of activation. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 285.6 KB | Display | ![]() |
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PDB format | ![]() | 194.1 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 703.1 KB | Display | ![]() |
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Full document | ![]() | 709.1 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8s93C ![]() 8s9fC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 76400.344 Da / Num. of mol.: 1 Mutation: E298A, K300A, E301A, A384P, S386P, T387P, A388P, L390F, K430R, L542M S543T, V555T, R562K, S564A, P565S, Y617P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P35991, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-9AJ / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 66.06 % Description: Monomer proteins at 18 mg/ml in 20 mM TRIS/HCl, pH 8.0, 150 mM NaCl, 10% glycerol 5 mM DTT were mixed with an equal volume of the precipitant solution, and then suspend over 0.25 ml of ...Description: Monomer proteins at 18 mg/ml in 20 mM TRIS/HCl, pH 8.0, 150 mM NaCl, 10% glycerol 5 mM DTT were mixed with an equal volume of the precipitant solution, and then suspend over 0.25 ml of precipitant solution. Leaf-shaped hexagonal crystals grew to up to 0.4 mm on a side after a period of two weeks. Crystals were frozen by transferring them, in six sequential steps, to a solution containing 0.1M Bis-Tris Propane, pH 7.5, 0.2M potassium thiocyanate, 20% PEG 3350 and 20% glycerol. |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion / pH: 7.5 Details: 20% PEG 3350, 0.1M Bis-Tris Propane, 0.2M potassium thiocyanate PH range: 7.2-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033167 Å / Relative weight: 1 |
Reflection | Resolution: 3.194→108.875 Å / Num. obs: 11550 / % possible obs: 79.61 % / Redundancy: 88.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.268 / Rpim(I) all: 0.029 / Rrim(I) all: 0.269 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 3.194→3.533 Å / Redundancy: 82.2 % / Rmerge(I) obs: 9.606 / Mean I/σ(I) obs: 2 / Num. unique obs: 577 / CC1/2: 0.743 / Rpim(I) all: 1.059 / Rrim(I) all: 9.665 / % possible all: 13.2 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 157.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→19.94 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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