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- PDB-8yvv: The Crystal Structure of BTK from Biortus -

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Basic information

Entry
Database: PDB / ID: 8yvv
TitleThe Crystal Structure of BTK from Biortus
ComponentsTyrosine-protein kinase BTK
KeywordsTRANSFERASE / Kinase / Serine/threonine-protein kinase / Stress response / Transcription / Transcription regulation / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


regulation of B cell cytokine production / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / regulation of B cell apoptotic process / eosinophil homeostasis / 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 / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / regulation of B cell apoptotic process / 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 / MyD88 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / positive regulation of immunoglobulin production / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of B cell differentiation / positive regulation of NLRP3 inflammasome complex assembly / phospholipase activator activity / negative regulation of interleukin-10 production / B cell activation / negative regulation of B cell proliferation / Fc-epsilon receptor signaling pathway / mesoderm development / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / RHO GTPases Activate WASPs and WAVEs / positive regulation of phagocytosis / positive regulation of B cell proliferation / cell maturation / FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calcium-mediated signaling / apoptotic signaling pathway / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Regulation of actin dynamics for phagocytic cup formation / G beta:gamma signalling through BTK / cellular response to reactive oxygen species / peptidyl-tyrosine phosphorylation / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / G alpha (12/13) signalling events / DAP12 signaling / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ER-Phagosome pathway / cytoplasmic vesicle / G alpha (q) signalling events / protein tyrosine kinase activity / adaptive immune response / Potential therapeutics for SARS / response to lipopolysaccharide / intracellular signal transduction / membrane raft / protein phosphorylation / innate immune response / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / 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 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 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
DI(HYDROXYETHYL)ETHER / Tyrosine-protein kinase BTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Pan, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of BTK from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Pan, W.
History
DepositionMar 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)62,7279
Polymers62,3022
Non-polymers4257
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-18 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.686, 102.995, 117.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 395 - 658 / Label seq-ID: 2 - 265

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 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: 31150.805 Da / Num. of mol.: 2
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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M LiCl2, 0.1M Tris pH8.0, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.25→34.33 Å / Num. obs: 27721 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 10.9
Reflection shellResolution: 2.25→2.32 Å / Rmerge(I) obs: 0.97 / Num. unique obs: 2516

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→32.976 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.209 / SU B: 8.051 / SU ML: 0.195 / Average fsc free: 0.945 / Average fsc work: 0.9639 / Cross valid method: FREE R-VALUE / ESU R: 0.343 / ESU R Free: 0.249
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2655 1368 4.945 %
Rwork0.2087 26296 -
all0.211 --
obs-27664 99.884 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 54.582 Å2
Baniso -1Baniso -2Baniso -3
1-0.323 Å2-0 Å2-0 Å2
2---1.895 Å20 Å2
3---1.572 Å2
Refinement stepCycle: LAST / Resolution: 2.25→32.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4173 0 25 220 4418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124298
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163950
X-RAY DIFFRACTIONr_angle_refined_deg0.8211.6455777
X-RAY DIFFRACTIONr_angle_other_deg0.2991.5619220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9435507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.526523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47310801
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.80610204
X-RAY DIFFRACTIONr_chiral_restr0.0430.2614
X-RAY DIFFRACTIONr_chiral_restr_other0.0090.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02875
X-RAY DIFFRACTIONr_nbd_refined0.1880.2827
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.23763
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22088
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.22105
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2168
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0880.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1120.210
X-RAY DIFFRACTIONr_nbd_other0.1130.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.27
X-RAY DIFFRACTIONr_mcbond_it2.3355.6932034
X-RAY DIFFRACTIONr_mcbond_other2.3345.6932034
X-RAY DIFFRACTIONr_mcangle_it3.7818.5172533
X-RAY DIFFRACTIONr_mcangle_other3.7818.522534
X-RAY DIFFRACTIONr_scbond_it2.4256.052264
X-RAY DIFFRACTIONr_scbond_other2.4246.0512265
X-RAY DIFFRACTIONr_scangle_it4.0968.9263242
X-RAY DIFFRACTIONr_scangle_other4.0958.9273243
X-RAY DIFFRACTIONr_lrange_it6.2470.0714927
X-RAY DIFFRACTIONr_lrange_other6.21368.9554898
X-RAY DIFFRACTIONr_ncsr_local_group_10.1020.057940
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.101820.0501
12AX-RAY DIFFRACTIONLocal ncs0.101820.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.25-2.3080.326950.30219080.30320040.920.93899.95010.302
2.308-2.3710.344940.26618530.2719470.9210.9511000.266
2.371-2.4390.336910.27118270.27419180.9380.9541000.271
2.439-2.5140.291870.25517530.25618410.9420.9699.94570.255
2.514-2.5960.323940.26217070.26518010.9290.9561000.262
2.596-2.6870.32980.25416240.25817230.930.95899.9420.254
2.687-2.7870.31740.23616110.23916850.9330.9631000.236
2.787-2.90.314990.23415440.23916430.9410.9641000.234
2.9-3.0280.263740.23514540.23615310.9560.96399.8040.235
3.028-3.1750.253790.2314180.23114970.9530.9681000.23
3.175-3.3450.283740.21613710.21914450.9480.971000.216
3.345-3.5450.292660.21612850.2213510.9560.9721000.216
3.545-3.7870.294590.20512010.20912610.9490.97599.92070.205
3.787-4.0860.245620.18811390.19112010.9680.9771000.188
4.086-4.4690.185420.16810590.16911030.9810.98299.81870.168
4.469-4.9850.209570.179480.17210060.9750.98199.90060.17
4.985-5.7340.292470.1938650.1989120.9560.9781000.193
5.734-6.9710.23370.2067440.2077820.980.97799.87210.206
6.971-9.6450.215260.1656030.1676290.9680.9821000.165
9.645-32.9760.298130.2143820.2174020.9580.96598.25870.214

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