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- PDB-7tdy: The ubiquitin-associated domain of human thirty-eight negative ki... -

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Basic information

Entry
Database: PDB / ID: 7tdy
TitleThe ubiquitin-associated domain of human thirty-eight negative kinase 1, flexibly fused to the 1TEL crystallization chaperone via a 2-glycine linker and crystallized at low protein concentration
ComponentsTranscription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
KeywordsONCOPROTEIN / Kinase / Ubiquitin-associated / chimera / chaperone
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / DNA-binding transcription repressor activity, RNA polymerase II-specific ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / protein tyrosine kinase activity / protein autophosphorylation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / protein phosphorylation / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. ...: / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Src homology 3 domains / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 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
FORMIC ACID / Transcription factor ETV6 / Non-receptor tyrosine-protein kinase TNK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsNawarathnage, S. / Bunn, D.R. / Stewart, C. / Doukev, T. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Structure / Year: 2023
Title: Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain.
Authors: Nawarathnage, S. / Tseng, Y.J. / Soleimani, S. / Smith, T. / Pedroza Romo, M.J. / Abiodun, W.O. / Egbert, C.M. / Madhusanka, D. / Bunn, D. / Woods, B. / Tsubaki, E. / Stewart, C. / Brown, S. ...Authors: Nawarathnage, S. / Tseng, Y.J. / Soleimani, S. / Smith, T. / Pedroza Romo, M.J. / Abiodun, W.O. / Egbert, C.M. / Madhusanka, D. / Bunn, D. / Woods, B. / Tsubaki, E. / Stewart, C. / Brown, S. / Doukov, T. / Andersen, J.L. / Moody, J.D.
History
DepositionJan 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0517
Polymers17,7751
Non-polymers2766
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Kim CA, Phillips ML, Kim W, Gingery M, Tran HH, Robinson MA, Faham S, Bowie JU. Polymerization of the SAM-domain of TEL in leukemogenesis and transcriptional repression. ...Evidence: electron microscopy, Kim CA, Phillips ML, Kim W, Gingery M, Tran HH, Robinson MA, Faham S, Bowie JU. Polymerization of the SAM-domain of TEL in leukemogenesis and transcriptional repression. EMBO J. 2001 Aug 1;20(15):4173-82.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.221, 67.221, 60.888
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1 / ETS translocation variant 6 / ETS-related protein Tel1 / Tel / CD38 negative kinase 1


Mass: 17775.053 Da / Num. of mol.: 1 / Mutation: R80S,V112E,C610A,C644A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, TNK1 / Plasmid: pET42_SUMO / Details (production host): N-term cleavable 10xHis / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B
References: UniProt: P41212, UniProt: Q13470, non-specific protein-tyrosine kinase
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.24 Å3/Da / Density % sol: 45.12 % / Description: Tapered hexagonal prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.2 uL of 2 mg/mL protein combined with 1.2 uL of 100 mM Bis-Tris, pH 7.00, 250 mM Mg-Formate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2021
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.53→33.61 Å / Num. obs: 22555 / % possible obs: 95.11 % / Redundancy: 18.8 % / Biso Wilson estimate: 29.3 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04884 / Rpim(I) all: 0.01144 / Rrim(I) all: 0.0502 / Net I/σ(I): 27.17
Reflection shellResolution: 1.53→1.585 Å / Redundancy: 14.9 % / Rmerge(I) obs: 1.029 / Mean I/σ(I) obs: 2.69 / Num. unique obs: 2344 / CC1/2: 0.907 / CC star: 0.975 / Rpim(I) all: 0.2728 / Rrim(I) all: 0.999 / % possible all: 99.96

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Processing

Software
NameVersionClassification
Cootv0.9model building
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Previous unpublished TNK1 UBA structure

Resolution: 1.53→33.61 Å / SU ML: 0.1798 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.5766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2174 1082 4.8 %
Rwork0.2052 21473 -
obs0.2058 22555 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.22 Å2
Refinement stepCycle: LAST / Resolution: 1.53→33.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 18 70 1230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01191190
X-RAY DIFFRACTIONf_angle_d1.16341609
X-RAY DIFFRACTIONf_chiral_restr0.0691177
X-RAY DIFFRACTIONf_plane_restr0.0052205
X-RAY DIFFRACTIONf_dihedral_angle_d11.7895413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.60.30491550.28632788X-RAY DIFFRACTION99.9
1.6-1.680.26051360.24162816X-RAY DIFFRACTION100
1.68-1.790.27451390.24612787X-RAY DIFFRACTION99.9
1.79-1.930.25951200.23472851X-RAY DIFFRACTION99.97
1.93-2.120.24181180.23192370X-RAY DIFFRACTION84.22
2.12-2.430.24961500.20412583X-RAY DIFFRACTION92.36
2.43-3.060.22811500.21262582X-RAY DIFFRACTION91.71
3.06-33.610.18241140.18882696X-RAY DIFFRACTION93.14
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)
16.259962002665.37223527576-2.178660788098.10036755425-2.059915384610.802387451642-0.003383664659660.136845282643-0.5287137212990.0243054425013-0.185549494852-0.3877385294150.02724082045280.1687683681930.1602592665480.2393078614740.0579662569614-0.03913990546750.207213003618-0.01380923932330.2368109053088.94859425172-24.8600023495-4.1627623534
22.075057727166.73776399747-2.14510447565.68263854418-2.225591629071.007041429320.208832718611-0.6767492531560.1707756973640.271234592064-0.3571921214960.198603368511-0.08372739712230.2407723819750.09989686174490.3206509749690.03418995232150.02144061695550.3431474181840.0342797340940.302270779449.34552846354-17.43472575792.57863783805
34.272110283180.913364190289-1.197185095262.00471962787-2.95948455971.03674368368-0.07112565224290.00036479008552-0.03765472901780.2105910086340.460195369730.503203894445-0.224501737186-0.234502919085-0.3672874518610.3111294200480.01977324232340.009257721094570.2476458351440.03675241668280.209387361862-1.87950432589-18.1420743617-3.80630232317
48.98186171592.13560657224-0.3474952843728.508496076091.599365981816.767183695120.1250682800810.2840331560690.478938280755-0.08511755414130.05598240853760.0334171805062-0.2077436198860.134043098946-0.1639933416420.2363323596390.01374204714870.01382741935060.1923335389820.04826112531110.2297871655555.94873898278-12.3983482237-6.07153388484
58.449289840982.73730154278-5.178186144063.54867055506-0.1733811062797.634272364890.343450914419-0.212165918558-0.0453249105270.40734129487-0.192581176543-0.162899224087-0.1866635440660.333820280772-0.09586672471880.2913405635790.0395070844756-0.1081955344380.309776371722-0.05881500213480.304738837641-8.21858572566-21.2401015144-10.5883626617
62.111048097130.3283644342980.3761017054146.52431318111.120318836227.77641873310.1112097796270.736756082736-0.3345874820190.0262745170049-0.1160487045730.1410976685670.516923737842-0.2107903230980.1101083272230.3659012907170.045461142243-0.04908723636320.379779039891-0.05464795809510.285855531925-12.5849942981-25.9905861463-15.753508659
72.1032851338.116472964050.07366398538549.998856063410.7469279452314.97356783665-0.1317009755170.446192700750.0833010562491-0.2296091900430.2181454972360.4556960678120.484798410922-0.228320490799-0.1176339010590.355157243990.0743684110928-0.07903398804660.362541750828-0.07795360641720.419368390717-22.929105337-24.35924941-14.8396105371
87.604871469232.872308249456.043300710149.129040276084.279089206582.085488857460.1568857345310.907170876606-0.196083173013-0.115816964073-0.1330867352630.4163103602060.298203678268-0.2397983832710.03456275075790.3608923806990.05464559117820.004992794240590.638495181171-0.09641468562290.429283761685-32.385133773-22.4765056902-16.5577426856
97.63762814437-1.580152649710.3986340025845.590553045830.4880807602494.60267714569-0.211347088572-1.060287478030.4033428064321.176801446380.3136257026780.2799435767830.378365042291-1.29656329709-0.05425483373560.5131595923610.02590244637140.01844613718560.822878676311-0.1606715870710.379606139518-31.6401728616-21.0544180539-7.74287938516
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 7 through 32 )7 - 321 - 26
22chain 'A' and (resid 33 through 45 )33 - 4527 - 39
33chain 'A' and (resid 46 through 53 )46 - 5340 - 47
44chain 'A' and (resid 54 through 77 )54 - 7748 - 71
55chain 'A' and (resid 78 through 90 )78 - 9072 - 84
66chain 'A' and (resid 91 through 109 )91 - 10985 - 103
77chain 'A' and (resid 110 through 125 )110 - 125104 - 119
88chain 'A' and (resid 126 through 139 )126 - 139120 - 133
99chain 'A' and (resid 140 through 154 )140 - 154134 - 148

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