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- PDB-2lf7: Intramolecular regulation of the ETS Domain within ETV6 sequence ... -

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Basic information

Entry
Database: PDB / ID: 2lf7
TitleIntramolecular regulation of the ETS Domain within ETV6 sequence R335 to Q436
ComponentsTranscription factor ETV6
KeywordsTRANSCRIPTION / auto-inhibition
Function / homology
Function and homology information


mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytosol
Similarity search - Function
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 ...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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor ETV6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 5
AuthorsCoyne III, H. / Green, S.M. / Graves, B.J. / Mcintosh, L.P.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Autoinhibition of ETV6 (TEL) DNA Binding: Appended Helices Sterically Block the ETS Domain.
Authors: Coyne, H.J. / De, S. / Okon, M. / Green, S.M. / Bhachech, N. / Graves, B.J. / McIntosh, L.P.
History
DepositionJun 28, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor ETV6


Theoretical massNumber of molelcules
Total (without water)13,0611
Polymers13,0611
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)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Transcription factor ETV6 / ETS translocation variant 6 / ETS-related protein Tel1 / Tel


Mass: 13060.987 Da / Num. of mol.: 1 / Fragment: ETS DNA binding domain residues 335-436
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Etv6, mouse ETV6, Tel, Tel1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P97360

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-13C NOESY
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D HN(CO)CA
1813D HNCO
1913D HBHA(CO)NH
11013D 1H-13C NOESY
1111dipsi3dn
1121Cmethyl NOESY
1131Nmethyl NOESY
1141ccctocsynnh
11512D 1H-15N HSQC
11612D 1H-13C HSQC aliphatic

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Sample preparation

DetailsContents: 50 mM sodium phosphate, 200 mM sodium chloride, 0.6 mM [U-99% 13C; U-99% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
200 mMsodium chloride-21
0.6 mMprotein-3[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 0.25 / pH: 5.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian UnityVarianUNITY5002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
TALOS+Cornilescu, Delaglio and Baxgeometry optimization
SparkyGoddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: iteration protocol used default values except iteration6 had the violation tolerance 0.09 violation threshold 0.5 and max_contribution 15, iteration7 set the violation threshold 0.07 ...Details: iteration protocol used default values except iteration6 had the violation tolerance 0.09 violation threshold 0.5 and max_contribution 15, iteration7 set the violation threshold 0.07 violation threshold 0.4 max_contributions 10. iteration 8 set the violation tolerance 0.05 violation threshold 0.3 max_contributions 5. The chemical shift tolerances were set to proton1=0.03 hetero1=0.4 proton2=0.3 and hetero2= 0.4. Violated restraints used in the calcuation were examined manually for correct identification as were restraints not used in the calculation over 3 angstroms. Long, medium, and short NOEs not used in the calcualtion were examined on refinement as were ambigous assigments with 3 or more contributions.
NMR constraintsNOE constraints total: 3787 / NOE intraresidue total count: 1397 / NOE long range total count: 1003 / NOE medium range total count: 665 / NOE sequential total count: 712 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 84 / Protein psi angle constraints total count: 84
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.05 Å / Maximum upper distance constraint violation: 0.22 Å

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