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- PDB-9o0h: The ubiquitin-associated domain of human thirty-eight negative ki... -

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Basic information

Entry
Database: PDB / ID: 9o0h
TitleThe ubiquitin-associated domain of human thirty-eight negative kinase 1, fused to the 3TEL crystallization chaperone via a 2-glycine linker
ComponentsTranscription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
KeywordsONCOPROTEIN / TELSAM / 3TEL / Pointed Domain / ETS / TEL / TNK1 / UBA Domain
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / Signaling by FLT3 fusion proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / 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 / neurogenesis / Signaling by FLT3 fusion proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / protein autophosphorylation / protein tyrosine kinase activity / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein phosphorylation / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / SAM domain-like / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 2. / Ets domain / ETS family ...: / : / SAM domain-like / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 2. / Ets domain / ETS family / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Transcription factor ETV6 / Non-receptor tyrosine-protein kinase TNK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsSamarawickrama, P. / Pedroza Romo, M.J. / Ludlow, K. / Keliiliki, A. / Doukov, T. / Moody, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM146209-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM155011-01 United States
CitationJournal: To Be Published
Title: 1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons
Authors: Samarawickrama, P. / Ludlow, K. / Probst, R. / Mead, D. / Doukov, T. / Moody, J.D.
History
DepositionApr 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1


Theoretical massNumber of molelcules
Total (without water)37,5961
Polymers37,5961
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.152, 65.540, 112.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1


Mass: 37595.590 Da / Num. of mol.: 1 / Fragment: TNK1 portion is the ubiquitin-associated domain
Mutation: V112E (Uniprot numbering) in the first ETV6 repeat, C610A,C644A (Uniprot numbering) in TNK1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, TNK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B
References: UniProt: P41212, UniProt: Q13470, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 54.99 % / Description: Thin rod
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.5M Ammonium Chloride, 0.1M BIS-TRISpropane pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2024
Details: Flat Si Rh coated M0,Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal monochromator, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.24→42.2 Å / Num. obs: 19277 / % possible obs: 93.63 % / Redundancy: 3.7 % / Biso Wilson estimate: 39.89 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.09231 / Rrim(I) all: 0.1967 / Net I/σ(I): 3.4
Reflection shellResolution: 2.244→2.324 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.581 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 1721 / CC1/2: 0.387 / CC star: 0.747 / Rpim(I) all: 0.8457 / Rrim(I) all: 1.807 / % possible all: 86.48

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→42.2 Å / SU ML: 0.3783 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.249 994 5.25 %
Rwork0.2244 17953 -
obs0.2257 18947 93.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.77 Å2
Refinement stepCycle: LAST / Resolution: 2.24→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 0 89 2470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242444
X-RAY DIFFRACTIONf_angle_d0.49073321
X-RAY DIFFRACTIONf_chiral_restr0.0369365
X-RAY DIFFRACTIONf_plane_restr0.0042416
X-RAY DIFFRACTIONf_dihedral_angle_d10.8222856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.360.34591430.34252338X-RAY DIFFRACTION87.89
2.36-2.510.37231330.29332633X-RAY DIFFRACTION96.44
2.51-2.70.33911320.28672601X-RAY DIFFRACTION97.16
2.7-2.980.29481490.26662596X-RAY DIFFRACTION95.28
2.98-3.410.29671530.24492551X-RAY DIFFRACTION94.15
3.41-4.290.21361440.17722540X-RAY DIFFRACTION91.92
4.29-42.20.18831400.1912694X-RAY DIFFRACTION92.83
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)
11.51858400752-2.12491985515-0.4697953079085.190370796281.243558118151.099239855930.06720193808920.172046887174-0.0355882367183-0.0806804957836-0.128535230823-0.00826134128777-0.01840895986280.07652391254750.05040129709230.429708509701-0.0517819237184-0.003366367118640.407146448682-0.002973997130240.27402930550231.2979938703-46.4961029421-76.1225797556
22.35868447779-0.205121254169-1.881986447340.7345177542251.195742781264.918562479620.0334144159562-0.162265218065-0.01686129648810.0712095527125-0.006982879850810.04855644586730.000735042405693-0.0168901294097-0.03394146403980.425397325503-0.0119136392748-0.0136241553040.3118571118470.01921699945740.30417056079920.0392083264-31.6020453352-53.6932241368
36.21155108117-1.726804483611.694039153076.75150051484-5.132211674136.137972666620.3938526303290.603587739521-0.312116765214-0.458722791897-0.544256126770.0961619212809-0.06314423845840.6027584894360.1320968481520.8297560820050.0560659413573-0.1189155381930.7035172610.1277377363930.50210868259830.9766512461-43.1892239002-23.7234949862
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 2 through 130 )2 - 1301 - 120
22chain 'B' and (resid 131 through 265 )131 - 265121 - 249
33chain 'B' and (resid 266 through 322 )266 - 322250 - 306

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