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- PDB-4y94: Crystal structure of the PH-TH module of Bruton's tyrosine kinase... -

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Basic information

Entry
Database: PDB / ID: 4y94
TitleCrystal structure of the PH-TH module of Bruton's tyrosine kinase bound to inositol hexakisphosphate
ComponentsNon-specific protein-tyrosine kinase
KeywordsTRANSFERASE / Btk / PH domain / tyrosine kinase / inositol hexakisphosphate
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 / 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 HEXAKISPHOSPHATE / Tyrosine-protein kinase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsWang, Q. / Kuriyan, J.
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 1.1Oct 14, 2020Group: Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity_src_gen / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Non-specific protein-tyrosine kinase
C: Non-specific protein-tyrosine kinase
A: Non-specific protein-tyrosine kinase
D: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,86714
Polymers80,6454
Non-polymers4,22210
Water77543
1
A: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5474
Polymers20,1611
Non-polymers1,3853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8873
Polymers20,1611
Non-polymers7252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8873
Polymers20,1611
Non-polymers7252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5474
Polymers20,1611
Non-polymers1,3853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.203, 64.012, 80.029
Angle α, β, γ (deg.)82.080, 88.790, 89.890
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA2 - 999
211chain BB0 - 999
311chain CC2 - 999
411chain DD0 - 999

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Components

#1: Protein
Non-specific protein-tyrosine kinase


Mass: 20161.178 Da / Num. of mol.: 4 / Fragment: PH domain (UNP residues 1-170)
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-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 1500, 0.1 M DL-malic acid, 3 mM potasium myo-inositol hexakisphosphate
PH range: 6.5

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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 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 30522 / % possible obs: 94.9 % / Redundancy: 2 % / Biso Wilson estimate: 52.82 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.055 / Rrim(I) all: 0.082 / Χ2: 0.987 / Net I/av σ(I): 10.82 / Net I/σ(I): 12.4 / Num. measured all: 61653
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.31-2.391.70.53823140.5540.5190.7480.78771.8
2.39-2.491.90.47829730.6590.4570.6630.7992.7
2.49-2.620.34730630.7750.3260.4770.84896.7
2.6-2.742.10.25631800.860.2390.3510.94897.5
2.74-2.912.10.18331410.9280.1710.2511.09397.7
2.91-3.132.10.12131510.9690.1120.1660.9498.1
3.13-3.452.10.0831460.9830.0740.1091.05498.4
3.45-3.952.10.05731820.9890.0510.0771.20198.7
3.95-4.982.10.04231930.9930.0380.0571.01398.8
4.98-5020.04231790.9950.0370.0561.02498.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementResolution: 2.4→46.483 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 1855 6.64 %
Rwork0.2294 26072 -
obs0.2311 27927 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.62 Å2 / Biso mean: 56.9964 Å2 / Biso min: 24.57 Å2
Refinement stepCycle: final / Resolution: 2.4→46.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 220 43 5393
Biso mean--87.67 58.12 -
Num. residues----617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065466
X-RAY DIFFRACTIONf_angle_d1.1677442
X-RAY DIFFRACTIONf_chiral_restr0.064796
X-RAY DIFFRACTIONf_plane_restr0.009900
X-RAY DIFFRACTIONf_dihedral_angle_d15.982131
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3082X-RAY DIFFRACTION10.092TORSIONAL
12B3082X-RAY DIFFRACTION10.092TORSIONAL
13C3082X-RAY DIFFRACTION10.092TORSIONAL
14D3082X-RAY DIFFRACTION10.092TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.46490.36691400.31881948208893
2.4649-2.53740.34311360.30111925206196
2.5374-2.61930.32751460.28652010215697
2.6193-2.71290.34931390.25572001214098
2.7129-2.82150.28051480.26281999214798
2.8215-2.94990.34481410.24932007214898
2.9499-3.10540.27731450.24282029217498
3.1054-3.29990.281390.2442011215098
3.2999-3.55470.24961460.22592021216799
3.5547-3.91220.26661420.22052029217199
3.9122-4.47790.20961390.20622032217199
4.4779-5.64010.21761420.21122033217599
5.6401-46.49220.23791520.222027217999

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