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- PDB-7t8j: The ubiquitin-associated domain of human thirty-eight negative ki... -

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Basic information

Entry
Database: PDB / ID: 7t8j
TitleThe ubiquitin-associated domain of human thirty-eight negative kinase-1 flexibly fused to the 1TEL crystallization chaperone via a GSGG linker
ComponentsTranscription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
KeywordsONCOPROTEIN / Protein polymer / Ubiquitin-associated domain / Helix bundle / Chimera
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / 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 ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / protein tyrosine kinase activity / protein autophosphorylation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / protein phosphorylation / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. ...: / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / ETS family / Ets-domain signature 2. / Ets domain / 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
Transcription factor ETV6 / Non-receptor tyrosine-protein kinase TNK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSoleimani, S. / Pedroza Romo, M.J. / Smith, T. / Brown, S. / Doukov, T. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Structure / Year: 2023
Title: Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain.
Authors: Nawarathnage, S. / Tseng, Y.J. / Soleimani, S. / Smith, T. / Pedroza Romo, M.J. / Abiodun, W.O. / Egbert, C.M. / Madhusanka, D. / Bunn, D. / Woods, B. / Tsubaki, E. / Stewart, C. / Brown, S. ...Authors: Nawarathnage, S. / Tseng, Y.J. / Soleimani, S. / Smith, T. / Pedroza Romo, M.J. / Abiodun, W.O. / Egbert, C.M. / Madhusanka, D. / Bunn, D. / Woods, B. / Tsubaki, E. / Stewart, C. / Brown, S. / Doukov, T. / Andersen, J.L. / Moody, J.D.
History
DepositionDec 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Refinement description / Category: refine / software / Item: _refine.pdbx_starting_model / _software.version
Revision 2.0Mar 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / struct / struct_ref_seq_dif
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _citation.title / _entity.formula_weight / _entity.pdbx_mutation / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct.title / _struct_ref_seq_dif.mon_id
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.3Dec 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9552
Polymers17,9191
Non-polymers351
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: This assembly is observed in all crystal structures of the 1TEL domain and was previously confirmed by electron microscopy (Kim et al. EMBO J. 2001 Aug 1;20(15):4173-82). The assembly can ...Evidence: This assembly is observed in all crystal structures of the 1TEL domain and was previously confirmed by electron microscopy (Kim et al. EMBO J. 2001 Aug 1;20(15):4173-82). The assembly can be generated by generating the crystallographic symmetry mates.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.651, 68.651, 56.735
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 Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1 / ETS translocation variant 6 / ETS-related protein Tel1 / Tel / CD38 negative kinase 1


Mass: 17919.182 Da / Num. of mol.: 1 / Mutation: R80S,V112E,C610A,C644A
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): N-term cleavable 10xHis-SUMO tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B
References: UniProt: P41212, UniProt: Q13470, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.06 % / Description: Teardrop with hexagonal cross-section
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.2 uL of 1 mg/mL protein in 50 mM Tris pH 8.8, 200 mM KCl combined with 1.2 uL of 100 mM Bis-tris-propane, 2.5 M Ammonium Nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2021
Details: Mirror: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.89→34.33 Å / Num. obs: 12236 / % possible obs: 99.92 % / Redundancy: 14 % / Biso Wilson estimate: 39.92 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06456 / Rpim(I) all: 0.0179 / Rrim(I) all: 0.06703 / Net I/av σ(I): 20.93 / Net I/σ(I): 20.93
Reflection shellResolution: 1.89→1.959 Å / Redundancy: 14.6 % / Rmerge(I) obs: 1.631 / Mean I/σ(I) obs: 2.59 / Num. unique obs: 1208 / CC1/2: 0.903 / CC star: 0.974 / Rpim(I) all: 0.4415 / Rrim(I) all: 0.99 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHASER1.19.2_4158phasing
autoPROC20210420data scaling
PHASER1.19.2-4158-000phasing
Coot0.9.6 ELmodel building
autoPROC20210420data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TCY

7tcy


Resolution: 1.89→34.33 Å / SU ML: 0.1493 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.0752
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2347 595 4.87 %
Rwork0.2238 11633 -
obs0.2243 12228 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.32 Å2
Refinement stepCycle: LAST / Resolution: 1.89→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 1 19 1115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331121
X-RAY DIFFRACTIONf_angle_d0.54441524
X-RAY DIFFRACTIONf_chiral_restr0.0365173
X-RAY DIFFRACTIONf_plane_restr0.0036191
X-RAY DIFFRACTIONf_dihedral_angle_d9.8708375
LS refinement shellResolution: 1.89→2.08 Å
RfactorNum. reflection% reflection
Rfree0.3643 147 4.05 %
Rwork0.3068 2887 -
obs--99.93 %
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)
15.56996578189-5.313475707685.909572198975.57048345483-4.577791125239.79252934514-0.0345017857171-0.3893284938740.9989548991060.225550151621-0.499237988088-2.41834936344-0.139241635030.9707810524590.4568389843550.372920581126-0.097613519313-0.05662547233480.5372184459290.01404588936860.802522122931-5.52131048994-50.9549081973-10.8141706267
29.75377167467-1.24089632198-1.265022051852.67192510661-5.999609668339.220931875050.1018222378770.4446061922690.454974740955-0.567166083771-0.417093942691-1.0595855199-0.02111555374440.6392906631870.3300432004360.350070754171-0.01041880718560.06511436639590.3725639959030.005258665135450.401064020172-8.01376255748-57.505158005-16.6002786412
39.41081716529-3.366818553280.1687473733376.33523021047-2.128290898387.79212738257-0.1985456491081.16469290822-0.158120004742-0.658630688837-0.229708645072-0.547541594211-0.333346315639-0.01101179383760.4723715647640.36464075573-0.06165698916580.01113238574540.4228938339720.02490593509130.370143417226-13.1022030244-65.0660920482-17.8714063499
44.85419026530.974731795866-0.8334268693268.98878294891-3.132019367772.984481455190.2433046463670.276930304617-0.1059865201060.0170542269938-0.193252667118-0.8518788280280.25025130232-0.01324530266060.08520696310940.3311973056470.00541394362111-0.05640792760710.3304275775620.023521819320.329432304126-17.3897942706-50.0301622264-18.2272620229
55.93660312537-0.143999195304-1.547527239522.24433131079-2.085942138755.879226532160.009293949727860.330430599401-0.0144406678997-0.659448483825-0.04442192890720.6096693263870.517121630191-0.2551651727570.003734477721480.353389618432-0.00880127056373-0.08415000469020.3013295783860.02111185330630.275941005673-23.309978702-59.2857891739-17.5857134552
62.337016784335.61601423547.536562088122.314749132177.426859189242.609156257-0.186834704518-0.445395452510.4762434217260.438613157807-0.2656897086430.530833662730.32527019703-0.02229910407520.5365838823050.3361271128910.03293863806060.01765514764510.353822689620.02725199847130.370293438509-17.1069354022-57.0746244933-8.17378835719
78.45350252471-5.497679862663.647321916946.68899680815-5.954301038068.230889907430.4144164491760.395539306354-1.15967185987-0.0646079520884-0.5931320507270.3459543389050.5556534716470.622224755209-0.1375124203280.4439762945850.0300047428019-0.1109652032540.36922309956-0.1065436591210.613168543822-19.7571434714-41.8583173639-6.07183002759
89.47931080178-0.4879140334225.6900051674910.00459355883.242289469538.38859069093-0.486760286775-0.2963533839050.7461285578081.27579147256-0.189443116655-0.599566697328-0.3171174617310.4782648038180.9360668494820.593624925476-0.0479587940156-0.1551586006260.521420128283-0.09610611052740.648780927357-19.282163664-33.5415277231-3.70379567869
98.231960237834.071169857531.809780699419.22379820116-1.594568667258.202771223890.1916426368360.09172119212250.6772119499750.614317607776-0.6991647832991.34880122596-0.472892109144-0.1710772663190.4790613633470.3998043031110.0220855919794-0.08502052231050.532806182895-0.2413739732070.749515291395-24.8238576446-25.1998835148-3.55028715378
100.157752215913-0.241120456916-0.1623114929614.47084478135-5.527621437358.092405281060.404794181692-0.461967438132-0.01215842285911.815794082360.8089784988451.81612348111-1.62310877161-1.58812866945-1.106442318060.9577686557450.3476869912710.1697208760910.83881737826-0.09834091855841.60846028846-31.7064121802-18.7985112771-1.3120831383
112.10879462651-2.76035407447-1.243075341423.15854336134-2.237791023795.808357539460.603488885956-0.1197345882340.404996022278-1.38837961930.2363299068682.079513121810.0685974284629-2.08836347389-0.9508474241250.8675461325880.164895356282-0.4241505410630.964890234009-0.03929803507331.09105541269-31.7562113626-22.1815320417-9.65544010701
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 3 through 17 )3 - 171 - 15
22chain 'A' and (resid 18 through 31 )18 - 3116 - 29
33chain 'A' and (resid 32 through 38 )32 - 3830 - 36
44chain 'A' and (resid 39 through 53 )39 - 5337 - 51
55chain 'A' and (resid 54 through 64 )54 - 6452 - 62
66chain 'A' and (resid 65 through 76 )65 - 7663 - 74
77chain 'A' and (resid 77 through 90 )77 - 9075 - 86
88chain 'A' and (resid 91 through 111 )91 - 11187 - 107
99chain 'A' and (resid 112 through 127 )112 - 127108 - 123
1010chain 'A' and (resid 128 through 141 )128 - 141124 - 137
1111chain 'A' and (resid 142 through 151 )142 - 151138 - 147

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