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- PDB-4y93: Crystal structure of the PH-TH-kinase construct of Bruton's tyros... -

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Basic information

Entry
Database: PDB / ID: 4y93
TitleCrystal structure of the PH-TH-kinase construct of Bruton's tyrosine kinase (Btk)
ComponentsNon-specific protein-tyrosine kinase,Non-specific protein-tyrosine kinase
KeywordsTRANSFERASE / PH-TH / Btk / tyrosine kinase
Function / homology
Function and homology information


FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / DAP12 signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / B cell affinity maturation / positive regulation of cGAS/STING signaling pathway / cellular response to interleukin-7 / G alpha (12/13) signalling events / G beta:gamma signalling through BTK ...FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / DAP12 signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / B cell affinity maturation / positive regulation of cGAS/STING signaling pathway / cellular response to interleukin-7 / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / negative regulation of cytokine production / phospholipase activator activity / G alpha (q) signalling events / negative regulation of B cell proliferation / positive regulation of NLRP3 inflammasome complex assembly / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / cell maturation / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / T cell receptor signaling pathway / cytoplasmic vesicle / adaptive immune response / intracellular signal transduction / membrane raft / zinc ion binding / ATP binding / identical protein binding / nucleus / plasma membrane / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-746 / Tyrosine-protein kinase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.695 Å
AuthorsWang, Q. / Kuriyan, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI091580 United States
Howard Hughes Medical Institute (HHMI) United States
Cancer Research Institute United States
CitationJournal: Elife / Year: 2015
Title: Autoinhibition of Bruton's tyrosine kinase (Btk) and activation by soluble inositol hexakisphosphate.
Authors: Wang, Q. / Vogan, E.M. / Nocka, L.M. / Rosen, C.E. / Zorn, J.A. / Harrison, S.C. / Kuriyan, J.
History
DepositionFeb 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-specific protein-tyrosine kinase,Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5784
Polymers51,8931
Non-polymers6853
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.328, 78.647, 157.569
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Non-specific protein-tyrosine kinase,Non-specific protein-tyrosine kinase


Mass: 51892.578 Da / Num. of mol.: 1 / Fragment: UNP residues 1-168, 384-658
Mutation: L542M, S543T, V555T, R562K, S564A, P565S, and Y617P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: BTK / Production host: Escherichia coli (E. coli)
References: UniProt: Q3ZC95, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-746 / 4-tert-butyl-N-[2-methyl-3-(4-methyl-6-{[4-(morpholin-4-ylcarbonyl)phenyl]amino}-5-oxo-4,5-dihydropyrazin-2-yl)phenyl]benzamide / CGI1746


Mass: 579.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H37N5O4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200mM NaCl, 50mM MgCl2, 20% PEG3350, 1mM IP3 / PH range: 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.695→50 Å / Num. obs: 53359 / % possible obs: 99.2 % / Redundancy: 7.9 % / Biso Wilson estimate: 15.35 Å2 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.045 / Rrim(I) all: 0.129 / Χ2: 1.051 / Net I/av σ(I): 17.214 / Net I/σ(I): 9.8 / Num. measured all: 414976
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.695-1.767.50.77651690.8890.2930.8320.62198.7
1.76-1.837.70.60651940.9310.2240.6480.69898.5
1.83-1.917.80.48251810.9550.1760.5140.80198.6
1.91-2.027.90.30851900.9740.1130.3290.97198.5
2.02-2.147.80.21851880.9830.0810.2331.17499
2.14-2.317.80.1652390.9910.060.1711.43199.3
2.31-2.547.90.13152860.9910.0480.140.97899.6
2.54-2.917.90.11653520.9920.0430.1241.18899.9
2.91-3.6680.08853920.9950.0320.0941.32599.9
3.66-508.20.06656680.9970.0240.0711.245100

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.695→43.678 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 2000 3.75 %
Rwork0.1571 51357 -
obs0.1585 53357 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.17 Å2 / Biso mean: 28.8452 Å2 / Biso min: 6.57 Å2
Refinement stepCycle: final / Resolution: 1.695→43.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 82 518 4096
Biso mean--21.98 32.57 -
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083643
X-RAY DIFFRACTIONf_angle_d1.1564924
X-RAY DIFFRACTIONf_chiral_restr0.048519
X-RAY DIFFRACTIONf_plane_restr0.007620
X-RAY DIFFRACTIONf_dihedral_angle_d15.0161373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.695-1.73730.29361330.20623424355793
1.7373-1.78430.21841400.18453590373099
1.7843-1.83680.2061410.17333604374599
1.8368-1.89610.19711410.17043623376499
1.8961-1.96390.19681390.16433578371798
1.9639-2.04250.19731410.15553626376799
2.0425-2.13550.1961430.15273666380999
2.1355-2.2480.20241420.14593651379399
2.248-2.38890.18541430.141436813824100
2.3889-2.57330.18511440.142136893833100
2.5733-2.83220.17741440.155637023846100
2.8322-3.2420.21041470.152537633910100
3.242-4.0840.17821470.145137683915100
4.084-43.69280.19411550.170939924147100

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