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- PDB-2md5: Structure of uninhibited ETV6 ETS domain -

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Basic information

Entry
Database: PDB / ID: 2md5
TitleStructure of uninhibited ETV6 ETS domain
ComponentsTranscription factor ETV6
KeywordsTRANSCRIPTION / Protein / 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 / torsion angle dynamics
Model detailsclosest to the average, model6
AuthorsDe, S. / Mcintosh, L.P. / Chan, A.C. / Coyne, H.J. / Okon, M. / Graves, B.J. / Murphy, M.E.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Steric Mechanism of Auto-Inhibitory Regulation of Specific and Non-Specific DNA Binding by the ETS Transcriptional Repressor ETV6.
Authors: De, S. / Chan, A.C. / Coyne, H.J. / Bhachech, N. / Hermsdorf, U. / Okon, M. / Murphy, M.E. / Graves, B.J. / McIntosh, L.P.
History
DepositionAug 29, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: 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 / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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)12,4501
Polymers12,4501
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)10 / 100target function
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: 12450.353 Da / Num. of mol.: 1 / Fragment: unp residues 329-426 / Mutation: C334S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Etv6, Tel, Tel1 / Production host: Escherichia coli (E. coli) / 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
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D H(CCO)NH
1513D (H)CC(CO)NH
1613D (H)CCH-TOCSY
1713D HN(CA)CB
1813D 1H-15N NOESY
1912D 1H-13C HSQC aliphatic
11012D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 0.6 mM [U-99% 13C; U-99% 15N] protein, 0.02 mM sodium phosphate, 0.05 mM sodium chloride, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMentity-1[U-99% 13C; U-99% 15N]1
0.02 mMsodium phosphate-21
0.05 mMsodium chloride-31
Sample conditionsIonic strength: 0.11 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8501
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1655 / NOE long range total count: 472 / NOE medium range total count: 315 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 85 / Protein psi angle constraints total count: 88
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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