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- PDB-2juo: GABPa OST domain -

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Basic information

Entry
Database: PDB / ID: 2juo
TitleGABPa OST domain
ComponentsGA-binding protein alpha chain
KeywordsTRANSCRIPTION / OST / ubiquitin / transcription factor / NMR ensemble / GA-binding protein / DNA-binding / Nucleus / Transcription regulation
Function / homology
Function and homology information


Transcriptional activation of mitochondrial biogenesis / blastocyst formation / negative regulation of megakaryocyte differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / chromatin ...Transcriptional activation of mitochondrial biogenesis / blastocyst formation / negative regulation of megakaryocyte differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Transcription factor, GA-binding, alpha subunit / GA-binding protein alpha subunit, N-terminal / GA-binding protein alpha chain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain ...Transcription factor, GA-binding, alpha subunit / GA-binding protein alpha subunit, N-terminal / GA-binding protein alpha chain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
GA-binding protein alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsKang, H. / Nelson, M.L. / Mackereth, C.D. / Schaerpf, M. / Graves, B.J. / McIntosh, L.P.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Identification and structural characterization of a CBP/p300-binding domain from the ETS family transcription factor GABP alpha
Authors: Kang, H.S. / Nelson, M.L. / Mackereth, C.D. / Scharpf, M. / Graves, B.J. / McIntosh, L.P.
History
DepositionAug 31, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 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: GA-binding protein alpha chain


Theoretical massNumber of molelcules
Total (without water)9,9751
Polymers9,9751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein GA-binding protein alpha chain / GABP-subunit alpha


Mass: 9975.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gabpa, E4tf1a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q00422

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
3122D 1H-15N HSQC
2232D 1H-13C HSQC
3313D CBCA(CO)NH
3413D HNCO
3513D HNCA
3613D HN(CA)CB
3723D 1H-15N NOESY
3813D 1H-15N TOCSY
3913D (H)CCH-TOCSY
3101simultaneous CN NOESY
3111EZ-HMQC-NH2
3121N-CG spin echo
3131CO-CG spin echo
114215N IPAP
11523D HNHB
1162T1 T2 HNNOE
11723D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate, 20 mM sodium chloride, 1 mM [U-100% 13C; U-100% 15N] GABPa OST, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
220 mM sodium phosphate, 50 mM sodium chloride, 1 mM [U-100% 15N] GABPa OST, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
320 mM sodium phosphate, 50 mM sodium chloride, 1 mM [U-10% 13C; U-100% 15N] GABPa OST, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate1
20 mMsodium chloride1
1 mMGABPa OST[U-100% 13C; U-100% 15N]1
2 mMDTT1
20 mMsodium phosphate2
50 mMsodium chloride2
1 mMGABPa OST[U-100% 15N]2
2 mMDTT2
20 mMsodium phosphate3
50 mMsodium chloride3
1 mMGABPa OST[U-10% 13C; U-100% 15N]3
2 mMDTT3
Sample conditionspH: 7 / Temperature: 298.1 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.11Goddardcollection
TALOSCornilescu, Delaglio and Baxdata analysis
MOLMOLKoradi, Billeter and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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