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

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Basic information

Entry
Database: PDB / ID: 9nge
TitleThe ubiquitin-associated domain of human thirty-eight negative kinase-1 rigidly fused to a double trigger variant of the 1TEL crystallization chaperone
ComponentsTranscription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
KeywordsONCOPROTEIN / Ubiquitin associated domain / TNK1 / Human thirty-eight Negative Kinase 1 / Sterile Alpha Motif (SAM) of Human Translocation ETS Leukemia (TEL) / protein crystallization chaperone / TELSAM / ETV6 / TRANSCRIPTION / 1TEL Crystallization 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 / 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
: / DI(HYDROXYETHYL)ETHER / 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
AuthorsAverett, J.C. / Bradford, M.J. / Averett, B.J. / Hansen, D. / 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: The ubiquitin-associated domain of human thirty-eight negative kinase-1 rigidly fused to a double trigger variant of the 1TEL crystallization chaperone
Authors: Averett, J.C.
History
DepositionFeb 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 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)39,10710
Polymers38,6092
Non-polymers4988
Water63135
1
A: Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7407
Polymers19,3051
Non-polymers4366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3673
Polymers19,3051
Non-polymers622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.935, 77.487, 38.342
Angle α, β, γ (deg.)90.000, 106.990, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

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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: 19304.727 Da / Num. of mol.: 2
Mutation: R80S,L96E,V112E in ETV6, and L591V,C610A,C644A in TNK1 (Uniprot numbering)
Source method: isolated from a genetically manipulated source
Details: Fusion protein of 1TEL and the UBA domain of TNK1 / Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, TNK1 / Plasmid: pET42 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B
References: UniProt: P41212, UniProt: Q13470, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.46 Å3/Da / Density % sol: 50 % / Description: Elongated plates with sharply tapered ends
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene Glycol 3350
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: 2.02→36.67 Å / Num. obs: 21733 / % possible obs: 90.36 % / Redundancy: 5.1 % / Biso Wilson estimate: 42.82 Å2 / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.1166 / Rpim(I) all: 0.05681 / Rrim(I) all: 0.1301 / Net I/σ(I): 6.31
Reflection shellResolution: 2.02→2.092 Å / Redundancy: 4.8 % / Rmerge(I) obs: 2.776 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 1297 / CC1/2: 0.441 / CC star: 0.783 / Rpim(I) all: 1.405 / Rrim(I) all: 3.128 / % possible all: 56.03

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Processing

Software
NameVersionClassification
autoPROCdata scaling
autoPROCdata reduction
PHASERphasing
PHENIX1.20.1_4487refinement
PDB-REDOrefinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→36.67 Å / SU ML: 0.2497 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.255
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2301 1053 4.98 %
Rwork0.213 20102 -
obs0.2139 21155 90.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.95 Å2
Refinement stepCycle: LAST / Resolution: 2.02→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 25 35 2422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252440
X-RAY DIFFRACTIONf_angle_d0.46883322
X-RAY DIFFRACTIONf_chiral_restr0.0332372
X-RAY DIFFRACTIONf_plane_restr0.0043425
X-RAY DIFFRACTIONf_dihedral_angle_d13.7559852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.110.379940.36131708X-RAY DIFFRACTION62.03
2.11-2.220.33031280.27732693X-RAY DIFFRACTION97.11
2.22-2.360.25661340.24942492X-RAY DIFFRACTION89.96
2.36-2.540.29711320.25282714X-RAY DIFFRACTION96.93
2.54-2.80.24491440.232475X-RAY DIFFRACTION89.69
2.8-3.20.24081600.22522767X-RAY DIFFRACTION99.32
3.2-4.030.24411190.19422421X-RAY DIFFRACTION86.9
4.03-36.670.18471420.18872832X-RAY DIFFRACTION98.84
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)
19.32628401725-1.164006242820.3016739899255.947285498050.6985200481017.407310674470.489495613113-0.297427764001-1.070822335930.567922926695-0.235538291267-0.7842290317510.9893485707510.853445136445-0.07414173794960.492519893017-0.00369663272006-0.0738748467690.4504790133880.03033651084210.59081233029842.3141774586-38.54711482996.41565904949
25.830208469010.879296889755-2.477247345830.739914324857-1.499566992571.358100789710.082405017005-0.29019610836-0.4374506595360.13393177246-0.151447704064-0.179520343104-0.07189058025920.06705472207950.07079015119480.38936995624-0.0449226651321-0.02545824651760.343034500309-0.002522117964350.29390285209715.0125594957-44.602248181811.0058322022
38.698849473631.42286692663-3.652531648157.19873702248-2.611479158669.080913078940.1062772277920.2804802594790.9923048738760.138784673573-0.399091271757-0.0596256064213-2.038957010740.1758707594650.2164822738030.7512271068360.0832608253223-0.1346508469160.368661072941-0.01086455983810.41572177615541.2329053468-61.257109867319.1090497876
43.35794425296-1.571489951494.0666088217.29362711764-2.303660227724.942515759810.0732215819457-0.138961884171-0.3058824955830.543712256758-0.462047847219-1.08704141420.02220116009561.787114103610.5379856410870.3499149743690.0681761677996-0.1397885491420.7737001304910.08783924140580.64537866657251.1431277136-71.186703259920.442699234
56.92644320449-4.829656679555.746166653463.37407399292-4.802605286956.31303296297-0.1861825134160.4684219405310.4434788564740.208894442428-0.280118298997-0.431400062866-0.1569007241580.5003933622820.340163569210.3435322263620.0364009395357-0.03534987334180.3595223086980.04370318245960.28730726743630.0133788803-60.38440604733.05010248336
68.5160825818-2.476375647984.811778473715.58172750233-2.199182038258.31987902479-0.2342811992990.3001623108270.362532235784-0.0221671349768-0.1109092331110.0786439034435-0.7917822728110.3445716527270.2401196608460.3478077054970.03115161820980.02364844889420.2352024737610.04490015025860.2048212865113.2265445503-49.2308991006-7.34693509578
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 75 )AA13 - 751 - 63
22chain 'A' and (resid 76 through 165 )AA76 - 16564 - 153
33chain 'B' and (resid 14 through 64 )BE14 - 641 - 51
44chain 'B' and (resid 65 through 75 )BE65 - 7552 - 62
55chain 'B' and (resid 76 through 135 )BE76 - 13563 - 122
66chain 'B' and (resid 136 through 165 )BE136 - 165123 - 152

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