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- PDB-9yt9: A428D mutant of Bruton's tyrosine kinase -

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Basic information

Entry
Database: PDB / ID: 9yt9
TitleA428D mutant of Bruton's tyrosine kinase
ComponentsTyrosine-protein kinase BTK
KeywordsTRANSFERASE / kinase dead mutant / clinical mutation / autoinhibited kinase / SIGNALING PROTEIN
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 / proteoglycan catabolic process / eosinophil homeostasis / positive regulation of type III hypersensitivity / negative regulation of B cell activation / positive regulation of synoviocyte proliferation / neutrophil homeostasis ...regulation of B cell cytokine production / regulation of B cell apoptotic process / monocyte proliferation / positive regulation of interleukin-17A production / proteoglycan catabolic process / eosinophil homeostasis / positive regulation of type III hypersensitivity / negative regulation of B cell activation / positive regulation of synoviocyte proliferation / neutrophil homeostasis / histamine secretion by mast cell / negative regulation of leukocyte proliferation / positive regulation of type I hypersensitivity / positive regulation of cGAS/STING signaling pathway / cellular response to molecule of fungal origin / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / negative regulation of interleukin-10 production / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of B cell differentiation / MyD88-dependent toll-like receptor signaling pathway / phospholipase activator activity / positive regulation of immunoglobulin production / mesoderm development / Fc-epsilon receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate binding / B cell activation / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of B cell proliferation / RHO GTPases Activate WASPs and WAVEs / phospholipase binding / peptidyl-tyrosine phosphorylation / FCERI mediated Ca+2 mobilization / B cell receptor signaling pathway / positive regulation of phagocytosis / apoptotic signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calcium-mediated signaling / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / cellular response to reactive oxygen species / non-membrane spanning protein tyrosine kinase activity / Regulation of actin dynamics for phagocytic cup formation / positive regulation of interleukin-6 production / T cell receptor signaling pathway / positive regulation of tumor necrosis factor production / G beta:gamma signalling through BTK / DAP12 signaling / G alpha (12/13) signalling events / response to lipopolysaccharide / ER-Phagosome pathway / protein tyrosine kinase activity / cytoplasmic vesicle / Potential therapeutics for SARS / G alpha (q) signalling events / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / membrane raft / innate immune response / perinuclear region of cytoplasm / DNA-templated transcription / zinc ion binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / PH domain / : / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain ...Tyrosine-protein kinase BTK, SH3 domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein kinase BTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGajewski, S.
Funding support1items
OrganizationGrant numberCountry
Other private
Citation
Journal: Cancer Discov / Year: 2026
Title: Molecular and Structural Basis of Pan-Resistance to BTK Degraders and Inhibitors.
Authors: Sievers, Q. / Lu, H. / Cool, A. / Gajewski, S. / Kong, T. / Noviski, M.A. / Whelan, S. / Wang, Y. / Mendoza Navarrete, L. / Mi, X. / Ficici, E. / Mukerji, R. / Iuliano, J.N. / Ye, J. / ...Authors: Sievers, Q. / Lu, H. / Cool, A. / Gajewski, S. / Kong, T. / Noviski, M.A. / Whelan, S. / Wang, Y. / Mendoza Navarrete, L. / Mi, X. / Ficici, E. / Mukerji, R. / Iuliano, J.N. / Ye, J. / Sanchez Garcia De Los Rios, M. / Bousquet, H. / Tan, M. / Brathaban, N. / Narasappa, N. / Lu, Y.W. / Elechko, J. / Maron, M.I. / Phelps, C.B. / Rahman, J. / Notti, R.Q. / Sekeres, S. / Lamkin, E.N. / Bravo, E. / Alencar, A. / Ewalt, M.D. / Islam, P. / Mato, A.R. / Roeker, L. / Bhatt, S. / Taylor, J. / Thompson, M.C. / Hansen, G.M. / Abdel-Wahab, O.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase BTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6793
Polymers31,5551
Non-polymers1242
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.057, 71.566, 106.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Tyrosine-protein kinase BTK / Agammaglobulinemia tyrosine kinase / ATK / B-cell progenitor kinase / BPK / Bruton tyrosine kinase


Mass: 31555.221 Da / Num. of mol.: 1 / Mutation: A428D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTK, AGMX1, ATK, BPK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q06187, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12.5% MPD, 12.5% PEG 1000, 12.5% PEG 3350, 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM L-Fucose, 20 mM D-Xylose, 20 mM N-Acetyl-D-Glucosamine, 100 mM Tris, 100 mM BICINE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS4 X 4M / Detector: PIXEL / Date: Feb 25, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.8→42.77 Å / Num. obs: 27799 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 30.93 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.052 / Net I/σ(I): 8.4
Reflection shellResolution: 1.8→1.968 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 11443 / CC1/2: 0.304 / Rpim(I) all: 1.086 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.77 Å / SU ML: 0.2824 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8988
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2384 2000 7.22 %
Rwork0.2043 25684 -
obs0.2067 27684 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.55 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 8 113 2056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672005
X-RAY DIFFRACTIONf_angle_d0.77442712
X-RAY DIFFRACTIONf_chiral_restr0.049291
X-RAY DIFFRACTIONf_plane_restr0.0074342
X-RAY DIFFRACTIONf_dihedral_angle_d18.1115727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.4471390.44021789X-RAY DIFFRACTION99.28
1.85-1.890.38861400.36551803X-RAY DIFFRACTION99.85
1.89-1.950.3361400.30721784X-RAY DIFFRACTION99.43
1.95-2.010.29841420.24561837X-RAY DIFFRACTION99.95
2.01-2.090.20911410.20831791X-RAY DIFFRACTION100
2.09-2.170.25551420.22111827X-RAY DIFFRACTION100
2.17-2.270.32221360.28621744X-RAY DIFFRACTION95.97
2.27-2.390.27921440.20761850X-RAY DIFFRACTION100
2.39-2.540.24921420.18441833X-RAY DIFFRACTION100
2.54-2.730.20521430.18571845X-RAY DIFFRACTION100
2.73-3.010.2161430.19591827X-RAY DIFFRACTION99.9
3.01-3.440.2181470.18971882X-RAY DIFFRACTION99.95
3.44-4.340.21111460.16071880X-RAY DIFFRACTION99.95
4.34-42.770.22291550.2011992X-RAY DIFFRACTION99.77
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.23101877258-1.250382334452.733652288231.21447733934-0.1358530718635.76112357877-0.249866950140.125765609170.129276037773-0.09993972729140.079442273159-0.0637562029952-0.4355762887520.9004162449190.1578480958650.481115125685-0.00408538529692-0.001592488987230.725322069254-0.002227279836610.326784639684-10.6478593206-23.1867414497-2.64533897715
22.67848991111-0.2336440772980.8548924697071.99703047670.09472156184354.50226010105-0.03861297602530.61374982671-0.0498321579856-0.1880708944390.0629965766127-0.00230637935252-0.03153704240190.238451057487-0.02734980997290.227669279281-0.044808037137-0.01332664184990.261042577527-0.009066154017870.168341656554-17.211713625-24.503540774913.0518116094
33.558140846290.5730421612330.6152396253132.972466171180.7485567239471.08828897202-0.023938382661-0.07217476977840.06623589765120.06817059953220.0541803710388-0.153477018581-0.005355552838620.0492814562575-0.02107570834140.203364277380.00740396268825-0.01768041231010.135108087364-0.0118480053190.135672587605-13.4339369942-21.584633891129.9021575553
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 392 through 451 )392 - 4511 - 47
22chain 'A' and (resid 452 through 540 )452 - 54048 - 136
33chain 'A' and (resid 541 through 657 )541 - 657137 - 241

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