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- PDB-2lul: Solution NMR Structure of PH Domain of Tyrosine-protein kinase Te... -

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Basic information

Entry
Database: PDB / ID: 2lul
TitleSolution NMR Structure of PH Domain of Tyrosine-protein kinase Tec from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR3504C
ComponentsTyrosine-protein kinase Tec
KeywordsTRANSFERASE / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


tissue regeneration / regulation of platelet activation / Fc-epsilon receptor signaling pathway / Interleukin-3, Interleukin-5 and GM-CSF signaling / peptidyl-tyrosine autophosphorylation / FCERI mediated Ca+2 mobilization / integrin-mediated signaling pathway / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity ...tissue regeneration / regulation of platelet activation / Fc-epsilon receptor signaling pathway / Interleukin-3, Interleukin-5 and GM-CSF signaling / peptidyl-tyrosine autophosphorylation / FCERI mediated Ca+2 mobilization / integrin-mediated signaling pathway / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / phospholipid binding / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-tyrosine phosphorylation / T cell receptor signaling pathway / adaptive immune response / cytoskeleton / intracellular signal transduction / protein phosphorylation / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase Tec, 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. ...Tyrosine-protein kinase Tec, 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
Tyrosine-protein kinase Tec
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Xiao, R. / Janjua, H. / Hamilton, K. / Shastry, R. / Kohan, E. / Acton, T.B. / Everett, J.K. / Lee, H. / Pederson, K. ...Liu, G. / Xiao, R. / Janjua, H. / Hamilton, K. / Shastry, R. / Kohan, E. / Acton, T.B. / Everett, J.K. / Lee, H. / Pederson, K. / Huang, Y.J. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of PH Domain of Tyrosine-protein kinase Tec from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR3504C
Authors: Liu, G. / Xiao, R. / Janjua, H. / Hamilton, K. / Shastry, R. / Kohan, E. / Acton, T.B. / Everett, J.K. / Lee, H. / Pederson, K. / Huang, Y.J. / Montelione, G.T.
History
DepositionJun 15, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase Tec
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5952
Polymers19,5301
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Tyrosine-protein kinase Tec


Mass: 19529.594 Da / Num. of mol.: 1 / Fragment: PH domain residues 1-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSCTK4, TEC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK
References: UniProt: P42680, 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D (H)CCH-TOCSY
1913D C(CO)NH
11013D HBHA(CO)NH
11122D 1H-13C HSQC
11232D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.614 mM [U-100% 13C; U-100% 15N] hr3504c.023, 50 uM DSS, 10 mM DTT, 50 uM ZnSO4, 0.02 % NaN3, 100 mM NaCL, 20 mM MES pH 6.5, 1 X Proteinase Inhibitors, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
20.828 mM [U-5% 13C; U-100% 15N] hr3504c.025, 50 uM DSS, 10 mM DTT, 50 uM ZnSO4, 0.02 % NaN3, 100 mM NaCL, 20 mM MES pH 6.5, 1 X Proteinase Inhibitors, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
30.52 mM [U-5% 13C; U-100% 15N] hr3504c.027, 50 uM DSS, 10 mM DTT, 50 uM ZnSO4, 0.02 % NaN3, 100 mM NaCL, 20 mM MES pH 6.5, 1 X Proteinase Inhibitors, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.614 mMhr3504c.023-1[U-100% 13C; U-100% 15N]1
50 uMDSS-21
10 mMDTT-31
50 uMZnSO4-41
0.02 %NaN3-51
100 mMNaCL-61
20 mMMES pH 6.5-71
1 %Proteinase Inhibitors-81
10 %D2O-91
0.828 mMhr3504c.025-10[U-5% 13C; U-100% 15N]2
50 uMDSS-112
10 mMDTT-122
50 uMZnSO4-132
0.02 %NaN3-142
100 mMNaCL-152
20 mMMES pH 6.5-162
1 %Proteinase Inhibitors-172
10 %D2O-182
0.52 mMhr3504c.027-19[U-5% 13C; U-100% 15N]3
50 uMDSS-203
10 mMDTT-213
50 uMZnSO4-223
0.02 %NaN3-233
100 mMNaCL-243
20 mMMES pH 6.5-253
1 %Proteinase Inhibitors-263
10 %D2O-273
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospindata collection
VnmrJVariandata collection
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
REDCATValafar, Prestegardgeometry optimization
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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