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- PDB-9z2l: The ubiquitin-associated domain of human thirty-eight negative ki... -

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Basic information

Entry
Database: PDB / ID: 9z2l
TitleThe ubiquitin-associated domain of human thirty-eight negative kinase-1 rigidly fused to the 1TEL crystallization chaperone
ComponentsTranscription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
KeywordsONCOPROTEIN / Sterile Alpha Motif (SAM) of Human Translocation ETS Leukemia (TEL) / protein crystallization chaperone / TELSAM / ETV6 / TRANSCRIPTION / 1TEL Crystallization Chaperone / TNK1 / UBA / Ubiquitin-Associated Domain / Thirty-eight Negative Kinase-1
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 / non-membrane spanning protein tyrosine kinase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / non-membrane spanning protein tyrosine kinase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / non-specific protein-tyrosine kinase / DNA-binding transcription repressor activity, RNA polymerase II-specific / protein autophosphorylation / DNA-binding transcription activator activity, RNA polymerase II-specific / protein tyrosine kinase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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: 2.02 Å
AuthorsWilson, E.W. / Bradford, M.J. / Averett, J.C. / Averett, B.J. / Anderson, E. / Anderson, 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 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM155011 United States
CitationJournal: To Be Published
Title: Modulating the pH sensitivity of the TELSAM crystallization chaperone for increased solubility
Authors: Averett, J.C. / Bradford, M.J. / Wilson, E.W. / Yseng, Y.J. / Averett, B.J. / Anderson, E. / Anderson, A. / Samarawickrama, P. / Pedroza Romo, M.J. / Doukov, T. / Moody, J.D.
History
DepositionNov 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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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
B: Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6897
Polymers38,4632
Non-polymers2255
Water1,874104
1
A: Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3513
Polymers19,2321
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3384
Polymers19,2321
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.004, 77.854, 118.995
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 / ETS translocation variant 6 / ETS-related protein Tel1 / Tel / CD38 negative kinase 1


Mass: 19231.717 Da / Num. of mol.: 2 / Mutation: R46S,V78E,L90V,C109A,C143A
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): kanamycin resistant / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / Variant (production host): BL21(DE3)
References: UniProt: P41212, UniProt: Q13470, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.39 Å3/Da / Density % sol: 48.5 % / Description: Hexagonal Plate
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.6 M Magnesium Sulfate, 0.1 Sodium Acetate / Temp details: Room Temperature

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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 10, 2024
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 and M2
RadiationMonochromator: Si111 liquid nitrogen cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.02→59.5 Å / Num. obs: 18612 / % possible obs: 75 % / Redundancy: 11.1 % / Biso Wilson estimate: 37.93 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09214 / Rpim(I) all: 0.02762 / Rrim(I) all: 0.09641 / Net I/σ(I): 12.98
Reflection shellResolution: 2.02→2.092 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.451 / Mean I/σ(I) obs: 0.32 / Num. unique obs: 3382 / CC1/2: 0.456 / CC star: 0.791 / Rpim(I) all: 0.7623 / Rrim(I) all: 1.647 / % possible all: 10.95

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Processing

Software
NameVersionClassification
PDB-REDOrefinement
PHENIX1.20.1_4487refinement
autoPROC1.0.5data reduction
XDSdata scaling
PHASER1.20.1_4487phasing
Coot0.9.8.95 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→59.5 Å / SU ML: 0.2283 / Cross valid method: FREE R-VALUE / Phase error: 32.901
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2739 908 5.01 %
Rwork0.2307 17049 -
obs-17957 75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.71 Å2
Refinement stepCycle: LAST / Resolution: 2.02→59.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 9 104 2409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242364
X-RAY DIFFRACTIONf_angle_d0.40383227
X-RAY DIFFRACTIONf_chiral_restr0.0346364
X-RAY DIFFRACTIONf_plane_restr0.0031413
X-RAY DIFFRACTIONf_dihedral_angle_d10.8241802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
2.02-2.0920.5376135.080.393425610.95
2.15-2.310.28961100.288214557.41
2.31-2.540.3651620.2812312683.16
2.55-2.910.30221880.2727355794.64
2.91-3.640.27751930.2397356196.16
3.67-59.50.23962030.1947388297.47
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)
15.311316879135.95128555513-2.742731636847.28234011426-4.099928841373.13184099803-0.5624953690910.74019735338-1.41433137433-1.095256243210.344440302996-0.9777466201031.333887776620.3428255256670.00403106458870.8604502878460.158576579238-0.331699246270.610753916331-0.5059947421071.4107723094212.22547552416.82172650339.4600009812
21.784226633850.9585612650381.377109880413.304356464872.20424719834.263116386910.244897050467-0.265077347277-0.03355668618120.60620218856-0.184781353761-0.182179529370.380659657659-0.428476475812-0.1489496289080.3057663954590.00936665196557-0.02386853426130.2480775167630.05102512859760.2511578331866.2923914538918.70188261330.9883439535
37.114099054881.23141696771.27839339638.385284710170.721225042215.9809865730.2901615755220.5043725223121.12904867653-0.548572430306-0.114486876193-0.574262786239-1.339132755880.0151783017267-0.1225658453730.5782876174590.02152062605260.09029215939490.2460594743450.02443645334530.5046135228471.518449088260.19404772206939.4985064801
42.68858008571.53676991993-3.87768232251.52448666505-2.09519609748.728750810050.167628300923-0.006467491189840.1946233673440.03478436104320.03516281197860.0280690647521-0.3283192383570.138076523516-0.1790794783520.2121543749130.0183409788515-0.004522510768760.186219052650.02153276922410.18086478040413.36679717912.4703533713620.6547364615
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 14 through 28 )BB14 - 281 - 15
22chain 'B' and (resid 29 through 164 )BB29 - 16416 - 151
33chain 'A' and (resid 12 through 64 )AA12 - 641 - 53
44chain 'A' and (resid 65 through 165 )AA65 - 16554 - 154

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