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

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Basic information

Entry
Database: PDB / ID: 9zvu
TitleThe ubiquitin-associated domain of human thirty-eight negative kinase-1 rigidly fused to a double trigger variant of the 1TEL crystallization chaperone, alternate crystal form
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 / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / 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 / protein autophosphorylation / protein tyrosine kinase activity / DNA-binding transcription activator activity, RNA polymerase II-specific ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / 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 / protein autophosphorylation / protein tyrosine kinase activity / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / negative regulation of transcription by RNA polymerase II / DNA-templated transcription / ATP binding / membrane / nucleus / 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 / 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
D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / Transcription factor ETV6 / Non-receptor tyrosine-protein kinase TNK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.964 Å
AuthorsAverett, B.J. / Averett, J.C. / Wilson, E.W. / Bradford, M.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. / Moody, J.D.
History
DepositionDec 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: 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)40,28221
Polymers38,6092
Non-polymers1,67319
Water2,180121
1
A: Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,09310
Polymers19,3051
Non-polymers7889
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)20,18911
Polymers19,3051
Non-polymers88410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.213, 79.367, 119.173
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

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Protein , 1 types, 2 molecules AB

#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: 19304.727 Da / Num. of mol.: 2 / Fragment: TNK1 UBA domain,TNK1 UBA domain / Mutation: R80S,L96E,V112E,L591V,C610A,C644A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, TNK1 / Plasmid: pET42 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21
References: UniProt: P41212, UniProt: Q13470, non-specific protein-tyrosine kinase

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Non-polymers , 5 types, 140 molecules

#2: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Sodium Tartrate, 16% PEG 3350 Monodisperse / 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 6, 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: 1.964→59.59 Å / Num. obs: 26655 / % possible obs: 99.86 % / Redundancy: 11.1 % / Biso Wilson estimate: 33.64 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1301 / Rpim(I) all: 0.04046 / Rrim(I) all: 0.1364 / Net I/σ(I): 12.34
Reflection shellResolution: 1.964→2.035 Å / Redundancy: 10.6 % / Rmerge(I) obs: 2.288 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 2619 / CC1/2: 0.521 / CC star: 0.828 / Rpim(I) all: 0.7269 / Rrim(I) all: 2.404 / % possible all: 99.81

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.964→59.59 Å / SU ML: 0.2635 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9582
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2469 1297 4.87 %
Rwork0.211 25348 -
obs0.2127 26645 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.2 Å2
Refinement stepCycle: LAST / Resolution: 1.964→59.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 64 121 2503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352423
X-RAY DIFFRACTIONf_angle_d0.5223291
X-RAY DIFFRACTIONf_chiral_restr0.0401361
X-RAY DIFFRACTIONf_plane_restr0.0044425
X-RAY DIFFRACTIONf_dihedral_angle_d13.3275815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.964-2.040.36731270.33672775X-RAY DIFFRACTION99.83
2.04-2.140.28321350.24272791X-RAY DIFFRACTION100
2.14-2.250.25041450.20842788X-RAY DIFFRACTION100
2.25-2.390.25631470.20582782X-RAY DIFFRACTION100
2.39-2.570.25811460.22712759X-RAY DIFFRACTION99.97
2.57-2.830.271420.2052800X-RAY DIFFRACTION99.9
2.83-3.240.20191570.20132814X-RAY DIFFRACTION99.97
3.24-4.080.21441260.18662849X-RAY DIFFRACTION99.27
4.09-59.590.25891720.21422990X-RAY DIFFRACTION99.87
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)
17.55401702526-4.293780157045.788307926084.44788448908-4.118735250154.771032532560.2766376124060.7313122099180.375505319626-0.236738248696-0.484073051702-0.119053932135-0.02519155903130.7476368286340.2584134256790.2916081975310.0471274098543-0.04266505258970.2871062184790.03847766626970.286510421655-8.3027331256129.1534085869-35.1260552724
24.86458559764-1.056412095322.436413693918.0179949278-2.582514741795.362439220510.1950373207230.1280233323620.0268670295203-0.514130286074-0.3050774997-0.02499807695190.07558548119440.2916502665280.1540322768360.1412836910830.02913065040490.0004311096081360.22952399702-0.0532461051750.2389372619391.2324550984612.9342391398-17.5524959065
35.51791431151-2.26958295490.28071240313.49222206760.8675924991822.07856808787-0.558410886127-1.082790591351.083020679410.6839294276060.2968053064290.26585383156-1.3732068308-0.03828533730840.4717165634650.8755024611190.157603254409-0.1437606620050.502998202325-0.2953282626380.59756218719-4.117508966053.72136584268-33.9877344062
41.56685637143-1.14544659666-2.316954095241.427640621892.603529195796.570357769180.1268254879980.03294889862520.0707992614756-0.194780635542-0.0507945615631-0.0209217041329-0.37102811771-0.0263560240645-0.06087782948870.1834181977430.0205332568002-0.01837656409980.188686209865-0.01372722725010.241302285643-9.845585183612.41633036459-26.3669115978
57.19978881983-2.11307909102-0.484274168855.337216421990.4181386409423.148663604210.3530150985680.599876965222-0.65082931669-0.722087786166-0.08171207138720.4538169775421.157998948760.412845720356-0.2385006794110.6369621883510.15424308872-0.1677019239250.409567295077-0.03765733405430.389779268482-16.52808276524.4004928649-44.4812062128
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 76 through 100 )BE76 - 10065 - 89
22chain 'B' and (resid 101 through 164 )BE101 - 16490 - 153
33chain 'A' and (resid 13 through 28 )AA13 - 281 - 16
44chain 'A' and (resid 29 through 165 )AA29 - 16517 - 153
55chain 'B' and (resid 12 through 75 )BE12 - 751 - 64

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