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- PDB-1b55: PH DOMAIN FROM BRUTON'S TYROSINE KINASE IN COMPLEX WITH INOSITOL ... -

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Basic information

Entry
Database: PDB / ID: 1b55
TitlePH DOMAIN FROM BRUTON'S TYROSINE KINASE IN COMPLEX WITH INOSITOL 1,3,4,5-TETRAKISPHOSPHATE
ComponentsTYROSINE-PROTEIN KINASE BTK
KeywordsTRANSFERASE / PH DOMAIN / BTK MOTIF / ZINC BINDING / X-LINKED AGAMMAGLOBULINEMIA / TYROSINE-PROTEIN KINASE / INOSITOL 1 / 3 / 4 / 5-TETRAKISPHOSPHATE
Function / homology
Function and homology information


regulation of B cell cytokine production / regulation of B cell apoptotic process / monocyte proliferation / positive regulation of interleukin-17A production / eosinophil homeostasis / proteoglycan catabolic process / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell ...regulation of B cell cytokine production / regulation of B cell apoptotic process / monocyte proliferation / positive regulation of interleukin-17A production / eosinophil homeostasis / proteoglycan catabolic process / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell / neutrophil homeostasis / positive regulation of cGAS/STING signaling pathway / cellular response to molecule of fungal origin / positive regulation of type I hypersensitivity / MyD88 deficiency (TLR2/4) / cellular response to interleukin-7 / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of B cell differentiation / positive regulation of immunoglobulin production / phospholipase activator activity / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / positive regulation of NLRP3 inflammasome complex assembly / Fc-epsilon receptor signaling pathway / mesoderm development / phosphatidylinositol-3,4,5-trisphosphate binding / B cell activation / RHO GTPases Activate WASPs and WAVEs / phospholipase binding / cell maturation / positive regulation of B cell proliferation / FCERI mediated Ca+2 mobilization / positive regulation of phagocytosis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / peptidyl-tyrosine phosphorylation / cellular response to reactive oxygen species / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / apoptotic signaling pathway / calcium-mediated signaling / positive regulation of NF-kappaB transcription factor activity / Regulation of actin dynamics for phagocytic cup formation / positive regulation of interleukin-6 production / G beta:gamma signalling through BTK / positive regulation of tumor necrosis factor production / DAP12 signaling / G alpha (12/13) signalling events / T cell receptor signaling pathway / ER-Phagosome pathway / cytoplasmic vesicle / protein tyrosine kinase activity / response to lipopolysaccharide / G alpha (q) signalling events / Potential therapeutics for SARS / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / membrane raft / innate immune response / perinuclear region of cytoplasm / zinc ion binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Tyrosine-protein kinase BTK, SH3 domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / : / PH domain profile. ...Tyrosine-protein kinase BTK, SH3 domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / : / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / Tyrosine-protein kinase BTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDjinovic Carugo, K. / Baraldi, E. / Hyvoenen, M. / Lo Surdo, P. / Riley, A.M. / Potter, B.V.L. / O'Brien, R. / Ladbury, J.E. / Saraste, M.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Structure of the PH domain from Bruton's tyrosine kinase in complex with inositol 1,3,4,5-tetrakisphosphate.
Authors: Baraldi, E. / Djinovic Carugo, K. / Hyvonen, M. / Surdo, P.L. / Riley, A.M. / Potter, B.V. / O'Brien, R. / Ladbury, J.E. / Saraste, M.
History
DepositionJan 12, 1999Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSINE-PROTEIN KINASE BTK
B: TYROSINE-PROTEIN KINASE BTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0976
Polymers39,9662
Non-polymers1,1314
Water3,531196
1
A: TYROSINE-PROTEIN KINASE BTK
B: TYROSINE-PROTEIN KINASE BTK
hetero molecules

A: TYROSINE-PROTEIN KINASE BTK
B: TYROSINE-PROTEIN KINASE BTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,19412
Polymers79,9324
Non-polymers2,2628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Unit cell
Length a, b, c (Å)110.205, 110.205, 215.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-274-

HOH

21B-239-

HOH

31B-249-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.330795, 0.942714, -0.043176), (0.943695, 0.330633, -0.011059), (0.00385, -0.044403, -0.999006)
Vector: 1.59142, 0.54895, 109.50422)

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Components

#1: Protein TYROSINE-PROTEIN KINASE BTK / BRUTON'S AGAMMAGLOBULINEMIA TYROSINE KINASE / BTK


Mass: 19983.014 Da / Num. of mol.: 2 / Fragment: PH DOMAIN AND BTK MOTIF
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH INOSITOL 1,3,4,5-TETRAKISPHOSPHATE / Source: (gene. exp.) Homo sapiens (human) / Cell: B-LYMPHOCYTE / Cell line: BL21 / Plasmid: PBAT4-BTK3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q06187, EC: 2.7.1.112
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H16O18P4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.7 %
Crystal growpH: 4.9 / Details: pH 4.9
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 %(w/v)PEG40001reservoir
2100 mMNa acetate1reservoir
310 %(v/v)methanol1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.947
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.947 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 25487 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 61.2 Å2 / Rsym value: 0.044 / Net I/σ(I): 11.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.346 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 35 Å / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.346

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BTK

1btk


Resolution: 2.4→35 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.35 1294 5 %RANDOM
Rwork0.234 ---
obs-25487 96.5 %-
Solvent computationSolvent model: J. MOL. BIOL. (1975), 91, 201-228 / Bsol: 150 Å2 / ksol: 0.753 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 58 196 2964
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.02256064.1
X-RAY DIFFRACTIONt_angle_deg2.82475344.6
X-RAY DIFFRACTIONt_dihedral_angle_d21.80232860
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0291403.2
X-RAY DIFFRACTIONt_gen_planes0.0357748.3
X-RAY DIFFRACTIONt_it6.162283310
X-RAY DIFFRACTIONt_nbd0.17326815
Software
*PLUS
Name: TNT / Version: 5EB / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg2.87
X-RAY DIFFRACTIONt_plane_restr0.0358.3

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