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- PDB-2jv3: Ets-1 PNT domain (29-138) NMR structure ensemble -

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Basic information

Entry
Database: PDB / ID: 2jv3
TitleEts-1 PNT domain (29-138) NMR structure ensemble
ComponentsETS1 proto-oncogene
KeywordsTRANSCRIPTION / ETS-1 Pointed (PNT) Domain / MAP Kinase phosphorylation site / alpha-helical bundle / transcription factor / DNA-binding / Nucleus
Function / homology
Function and homology information


Oncogene Induced Senescence / pituitary gland development / regulation of extracellular matrix disassembly / response to laminar fluid shear stress / PML body organization / angiogenesis involved in wound healing / positive regulation of leukocyte adhesion to vascular endothelial cell / hypothalamus development / histone acetyltransferase binding / immune system process ...Oncogene Induced Senescence / pituitary gland development / regulation of extracellular matrix disassembly / response to laminar fluid shear stress / PML body organization / angiogenesis involved in wound healing / positive regulation of leukocyte adhesion to vascular endothelial cell / hypothalamus development / histone acetyltransferase binding / immune system process / estrous cycle / positive regulation of blood vessel endothelial cell migration / regulation of angiogenesis / response to mechanical stimulus / positive regulation of endothelial cell migration / response to interleukin-1 / positive regulation of erythrocyte differentiation / female pregnancy / cell motility / positive regulation of miRNA transcription / negative regulation of inflammatory response / cellular response to hydrogen peroxide / positive regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / response to estradiol / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / nucleic acid binding / cell differentiation / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / host cell nucleus / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / Ets-domain signature 1. ...Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein C-ets-1 / E26 avian leukemia oncogene 1, 5' domain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics, simulated annealing, MD, SA
Model detailsEts-1 PNT domain (residues 29-138), 25 structures.
AuthorsLee, G.M. / Kang, H. / Schaerpf, M. / Slupsky, C.M. / Lawrence, M.P.
Citation
Journal: To be Published
Title: Ets-1 PNT domain (29-138) NMR structure ensemble
Authors: Kang, H. / Nelson, M.L. / Lee, G.M. / Graves, B.J. / McIntosh, L.P.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structure of the Ets-1 pointed domain and mitogen-activated protein kinase phosphorylation site
Authors: Slupsky, C.M. / Gentile, L.N. / Donaldson, L.W. / Mackereth, C.D. / Seidel, J.J. / Graves, B.J. / McIntosh, L.P.
History
DepositionSep 11, 2007Deposition site: BMRB / Processing site: RCSB
SupersessionOct 16, 2007ID: 1BQV
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: ETS1 proto-oncogene


Theoretical massNumber of molelcules
Total (without water)12,5681
Polymers12,5681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ETS1 proto-oncogene / E26 avian leukemia oncogene 1 / 5' domain


Mass: 12567.518 Da / Num. of mol.: 1 / Fragment: Ets-1 PNT Domain (residues 29-138)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ets1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21 (de3) / References: UniProt: Q540Q5, UniProt: P27577*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Ets-1 PNT domain (residues 29-138), 25 structures.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CCC-TOCSY-NNH
1413D HCC-TOCSY-NNH
1513D (H)CCH-TOCSY
161simultaneous 3D 15N-13C-NOESY
171simultaneous 3D 15N-13C-NOESY (methyl)
1813D 1H-13C NOESY(aromatics)
1922D 1H-15N IPAP HSQC
NMR detailsText: The structure was solved with a combination of NOESY and RDC data.

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Sample preparation

Details
Solution-IDContentsSolvent system
1200-300 uM [U-100% 13C; U-100% 15N] EtsPnt, sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
2200-300 uM [U-100% 15N] EtsPnt, sodium phosphate, Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMEtsPnt, sodium phosphate[U-100% 13C; U-100% 15N]1
200 uMEtsPnt, sodium phosphate, Pf1 phage[U-100% 15N]2
Sample conditionsIonic strength: 20 / pH: 6.2 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.11Goddarddata analysis
MOLMOL2K2Koradi, Billeter and Wuthrichdata analysis
TALOS2003.027.13.05Cornilescu, Delaglio and Baxdata analysis
ProcheckNMR3.5.4Laskowski and MacArthurstructure solution
ProcheckNMR3.5.4Laskowski and MacArthurdata analysis
RefinementMethod: molecular dynamics, simulated annealing, MD, SA / Software ordinal: 1
Details: 10000 steps @ 10000K, time step = 0.003fs, 10000K -> 1000 K in 5000 steps (first stage); 1000 K -> 50K in 4000 steps (second stage). Final 25 structures refined in Aria water box.
NMR constraintsNOE constraints total: 3632 / NOE intraresidue total count: 932 / NOE long range total count: 995 / NOE medium range total count: 1014 / NOE sequential total count: 691 / Hydrogen bond constraints total count: 34 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 89 / Protein psi angle constraints total count: 89
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 2.909 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25 / Maximum torsion angle constraint violation: 12 ° / Torsion angle constraint violation method: CNS/ARIA

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