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- PDB-7u4w: The ubiquitin-associated domain of human thirty-eight negative ki... -

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Basic information

Entry
Database: PDB / ID: 7u4w
TitleThe ubiquitin-associated domain of human thirty-eight negative kinase-1 flexibly fused to the 1TEL crystallization chaperone via a 2-glycine linker and crystallized at traditional protein concentration
ComponentsTranscription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
KeywordsSIGNALING PROTEIN / 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 / 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 / cytosol / cytoplasm
Similarity search - Function
: / : / SAM domain-like / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / Ets-domain signature 2. / Ets domain ...: / : / SAM domain-like / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / 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 / DNA polymerase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
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: 2.1 Å
AuthorsNawarathnage, S. / Pedroza Romo, M.J. / Smith, T. / Bunn, D. / Stewart, C. / Doukov, T. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateInstitutional Startup 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
DepositionMar 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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 1.3Dec 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


Theoretical massNumber of molelcules
Total (without water)17,7751
Polymers17,7751
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Kim, C.A., Phillips, M.L., Kim, W., Gingery, M., Tran, H.H., Robinson, M.A., Faham, S. and Bowie, J.U. (2001), Polymerization of the SAM domain of TEL in leukemogenesis ...Evidence: electron microscopy, Kim, C.A., Phillips, M.L., Kim, W., Gingery, M., Tran, H.H., Robinson, M.A., Faham, S. and Bowie, J.U. (2001), Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression. The EMBO Journal, 20: 4173-4182. https://doi.org/10.1093/emboj/20.15.4173
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.971, 67.971, 55.749
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: 17775.053 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B
References: UniProt: P41212, UniProt: Q13470, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.19 % / Description: Tapered hexagonal prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.2 uL of 15 mg/mL protein combined with 1.2 uL of 100 mM Bis-Tris, pH 6.50, 750 mM 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: Dec 2, 2020
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.1→40.48 Å / Num. obs: 8522 / % possible obs: 98.32 % / Redundancy: 14.5 % / Biso Wilson estimate: 51.29 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04076 / Rpim(I) all: 0.01108 / Rrim(I) all: 0.04229 / Net I/σ(I): 28.14
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.088 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 820 / CC1/2: 0.923 / CC star: 0.98 / Rpim(I) all: 0.2973 / Rrim(I) all: 1.129 / % possible all: 96.24

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootv0.9model building
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QAR (for 1TEL), homology model (UBA)

2qar

1tel


Resolution: 2.1→40.48 Å / SU ML: 0.3045 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.1723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2756 467 5.5 %
Rwork0.2452 8026 -
obs0.2469 8493 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.8 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 0 9 1032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00381092
X-RAY DIFFRACTIONf_angle_d0.56521496
X-RAY DIFFRACTIONf_chiral_restr0.0368163
X-RAY DIFFRACTIONf_plane_restr0.0049194
X-RAY DIFFRACTIONf_dihedral_angle_d10.9578356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.40.36121480.32932637X-RAY DIFFRACTION97.65
2.4-3.030.341650.30482654X-RAY DIFFRACTION98.22
3.03-40.480.24711540.2212735X-RAY DIFFRACTION99.14
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)
18.122186347713.3584225261.138914995552.231271441311.327502669011.029555498881.64083292345-0.1572555727871.977295240781.314619659580.04457347899151.46373215998-2.160253262941.36945051439-1.765682589291.11678258056-0.1885023213740.2312278735650.570113442397-0.1335452358640.828018814379-22.978575697522.18759686861.89389984851
27.699355137823.140494837620.900128115099.68022644197-0.3276814893844.0741581793-0.2528966548930.101358390257-0.230866017754-0.07188745700660.232152861755-0.255877030221-0.03542108037570.185974613620.003618630330670.356631523266-0.00984987501817-0.01712693797720.371563342835-0.04724071467130.41624431228-12.498122636814.4991598236-2.49068320796
34.88500694155.10653654621-2.598815188435.66505551951-3.163314283562.60341397852-0.9238444852010.8003463498970.117695493649-2.12189443795-0.0598398454725-1.152185557790.2334861721720.651820985611.12221275940.6895918395570.01916276374390.1196715707090.6355703828620.07354727358620.919170989422-22.19844660023.852608378545.54295596148
43.377997341674.03731189556-4.274263711279.79044604232-3.870617850765.71796375974-0.106499063901-0.349520056478-1.04649593508-0.55108691106-1.13952745706-0.2275393931.113153923270.1431833042271.263941407260.7205862609690.1788747990610.2305196753390.6566663215710.0256133363610.70748022377-31.6619174377-3.543694074399.97105151456
55.66206425057-1.02789112012-0.1508904017782.63911246992.126107929893.569229397750.965957183187-0.8820114174380.54628400237-0.207995383642-0.640126039396-1.455147336870.8972391322760.509214356691-0.1588730224671.26880552848-0.06546084388630.623962054950.5197891725040.1736172781541.62927268065-35.615928247-18.072542862611.5608696742
63.83300506984-3.756876416322.889452505525.23550611374-6.466184320632.00159243045-0.0811223665407-0.347049692632-1.09914428717-1.324502312510.770079099971-0.1347838375240.757307000114-0.622896790281-0.2725182383951.556028203920.181703508050.8360029349630.6615913967720.09168418420951.47613537389-32.4600049986-16.95994848944.1848905422
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 6 through 12 )6 - 121 - 7
22chain 'A' and (resid 13 through 75 )13 - 758 - 70
33chain 'A' and (resid 76 through 90 )76 - 9071 - 83
44chain 'A' and (resid 91 through 126 )91 - 12684 - 119
55chain 'A' and (resid 127 through 139 )127 - 139120 - 132
66chain 'A' and (resid 140 through 151 )140 - 151133 - 144

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