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

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Basic information

Entry
Database: PDB / ID: 9cpl
TitleThe ubiquitin-associated domain of human thirty-eight negative kinase 1, fused to the 2TEL crystallization chaperone via a 2-glycine linker
Components2TEL/Non-receptor tyrosine-protein kinase TNK1 fusion protein
KeywordsONCOPROTEIN / TELSAM / 2TEL / Pointed Domain / ETS / TEL / TNK1 / UBA Domain / Broken Periodicity
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 / 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 / nucleus / membrane / 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
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: 2.4 Å
AuthorsSamarawickrama, P. / Averett, J. / Doukov, T. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM146209-01 United States
CitationJournal: To Be Published
Title: 1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons
Authors: Samarawickrama, P. / Ludlow, K. / Probst, R. / Abiodun, W. / Averett, J. / Hansen, D. / Doukov, T. / Moody, J.D.
History
DepositionJul 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2TEL/Non-receptor tyrosine-protein kinase TNK1 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1392
Polymers29,0931
Non-polymers461
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.725, 105.725, 50.917
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 2TEL/Non-receptor tyrosine-protein kinase TNK1 fusion protein


Mass: 29092.832 Da / Num. of mol.: 1
Mutation: First TELSAM:R80S,V112E,Second TELSAM: R80S,UBA Domain: C610A,C644A
Source method: isolated from a genetically manipulated source
Details: Tandem fusion of Two TELSAM Domains followed by TNK1 domain
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, TNK1 / Plasmid: pET42-His-2TEL-XhoI / Details (production host): N-term 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.: 1 / Source method: isolated from a natural source / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.83 Å3/Da / Density % sol: 56.48 % / Description: clusters of rice-shaped crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100mM BisTris, pH 6.0, 960mM 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: Aug 25, 2023 / Details: Rh coated collimating mirror, K-B focusing mirrors
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: 2.4→45.78 Å / Num. obs: 12862 / % possible obs: 99.12 % / Redundancy: 10.2 % / Biso Wilson estimate: 68.73 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1028 / Rpim(I) all: 0.03386 / Rrim(I) all: 0.1083 / Net I/σ(I): 10.88
Reflection shellResolution: 2.4→2.4 Å / Redundancy: 10.2 % / Rmerge(I) obs: 3.597 / Mean I/σ(I) obs: 0.62 / Num. unique obs: 1150 / CC1/2: 0.449 / CC star: 0.787 / Rpim(I) all: 1.173 / Rrim(I) all: 3.786 / % possible all: 92

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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: 2.4→45.78 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2634 713 5.58 %
Rwork0.2294 12070 -
obs0.2313 12783 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.94 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 3 17 1795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341841
X-RAY DIFFRACTIONf_angle_d0.48012504
X-RAY DIFFRACTIONf_chiral_restr0.0369272
X-RAY DIFFRACTIONf_plane_restr0.0041317
X-RAY DIFFRACTIONf_dihedral_angle_d10.77641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.580.36421580.35432277X-RAY DIFFRACTION94.71
2.58-2.840.38481520.29912397X-RAY DIFFRACTION99.96
2.84-3.250.37881400.32412434X-RAY DIFFRACTION99.96
3.25-4.10.25981120.23542466X-RAY DIFFRACTION100
4.1-45.780.21361510.1832496X-RAY DIFFRACTION99.77
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)
17.34509794456-2.21562849081-6.101102956490.9943870603942.410123543096.049122618160.2200014744390.479795485913-0.945008722505-0.439925333384-0.4829353522580.190043785899-0.703964678376-0.5179569732640.1440114104250.697586773690.03993628586890.02281794518440.6438256484090.05512686827360.617184102158-31.08123977-20.1639401076-12.5180262115
25.3273440286-0.798351291842-3.630961825932.503241341020.6101304121446.45070281090.3890267462110.945503290588-0.415875209572-0.266391160893-0.26601361501-0.176464236512-0.482649177580.197935700209-0.04831104111750.7112534626740.1836302048770.03566208531240.7758567565950.05318518243520.550291603516-12.3001554273-26.3216557561-31.3219425066
38.94524801384-1.470218191390.6136455046664.83486141045-1.633136585255.81621788532-0.126967850266-0.168327745045-0.03122320771170.04358634998490.2003349882070.261469058046-0.509781466358-0.257297388823-0.01809016992650.5863601033690.00927879790659-0.05635180423340.378025746475-0.01927109908760.475331134584-52.919820658-8.98365557114-7.63946223226
47.469938518070.0734209488661-0.4261938639724.1546064027-1.240554830483.75947465187-0.297092882727-1.16847820802-0.6005474009660.415561069073-0.481632820546-0.664745675293-0.1538944418591.324229619590.7381288888630.539102287531-0.0605047632494-0.003508386002420.886131320920.2581209097340.60398023791-34.6067489737-18.30202282690.812853101302
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 161 through 186 )161 - 186144 - 169
22chain 'A' and (resid 187 through 251 )187 - 251170 - 234
33chain 'A' and (resid 14 through 87 )14 - 871 - 74
44chain 'A' and (resid 88 through 160 )88 - 16075 - 143

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