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- PDB-2gd7: The Structure of the Cyclin T-binding domain of Hexim1 reveals th... -

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Basic information

Entry
Database: PDB / ID: 2gd7
TitleThe Structure of the Cyclin T-binding domain of Hexim1 reveals the molecular basis for regulation of transcription elongation
ComponentsHEXIM1 protein
KeywordsTRANSCRIPTION / Hexim1 / transcription regulation / transcription elongation / positive transcription elongation factor-b / P-Tefb NMR / structure determination / symmetric dimer / coiled coil / MAQ1 / CLP-1 / EDG1
Function / homology
Function and homology information


7SK snRNP / 7SK snRNA binding / snRNA binding / negative regulation of viral transcription / negative regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / protein kinase inhibitor activity / negative regulation of transcription elongation by RNA polymerase II / positive regulation of signal transduction by p53 class mediator / P-TEFb complex binding ...7SK snRNP / 7SK snRNA binding / snRNA binding / negative regulation of viral transcription / negative regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / protein kinase inhibitor activity / negative regulation of transcription elongation by RNA polymerase II / positive regulation of signal transduction by p53 class mediator / P-TEFb complex binding / activation of innate immune response / heart development / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2910 / HEXIM / Hexamethylene bis-acetamide-inducible protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, cartesian coordinate simulated annealing
AuthorsDames, S.A.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structure of the Cyclin T binding domain of Hexim1 and molecular basis for its recognition of P-TEFb.
Authors: Dames, S.A. / Schonichen, A. / Schulte, A. / Barboric, M. / Peterlin, B.M. / Grzesiek, S. / Geyer, M.
#1: Journal: To be Published
Title: NMR assignment of the Cyclin T-binding domain of human Hexim1
Authors: Dames, S.A. / Schoenichen, A. / Schulte, A. / Barboic, M. / Peterlin, M. / Grzesiek, S. / Geyer, M.
History
DepositionMar 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEXIM1 protein
B: HEXIM1 protein


Theoretical massNumber of molelcules
Total (without water)25,3602
Polymers25,3602
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein HEXIM1 protein / HMBA-inducible


Mass: 12680.050 Da / Num. of mol.: 2
Fragment: c-terminal Cyclin T-binding domain of human Hexim1 (residues 255-359)
Mutation: G256A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Hexim1 (255-359), G256A / Plasmid: pProEx-HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 5453682, UniProt: O94992*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 13C-separated NOESY
1243D 15N-separated NOESY
1363D 13C-filter-edit-NOESY
1443D HNHA, 3D HNHB
1523D HACAHB-COSY
1632D 15N-IPAP-HSQC, 3D HN(CA)CO
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy in solution.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM U-15N,13C, 20 mM potassium phosphate buffer, pH 7.2, 50 mM NaCl, 10mM TCEP/HCl, 1 mM DTE, 0.02% Na-azide, 95% H2O, 5% D2O95% H2O/5% D2O
20.6 mM U-15N,13C, 20 mM potassium phosphate buffer, pH 7.2, 50 mM NaCl, 10mM TCEP/HCl, 1 mM DTE, 0.02% Na-azide, 100% D2O100% D2O
30.6 mM U-15N,13C, 20 mM potassium phosphate buffer, pH 7.2, 50 mM NaCl, 10mM TCEP/HCl, 1 mM DTE, 0.02% Na-azide, 95% H2O, 5% D2O, 16 mg/ml PF1 phage95% H2O, 5% D2O, 16 mg/ml PF1 phage
41.2 mM U-15N, 20 mM potassium phosphate buffer, pH 7.2, 50 mM NaCl, 10mM TCEP/HCl, 1 mM DTE, 0.02% Na-azide, 95% H2O, 5% D2O95% H2O/5% D2O
50.6 mM 10% 13C, 20 mM potassium phosphate buffer, pH 7.2, 50 mM NaCl, 10mM TCEP/HCl, 1 mM DTE, 0.02% Na-azide, 95% H2O, 5% D2O95% H2O/5% D2O
60.5 mM U-15N,13C, 0.5 mM unlabeled, 20 mM potassium phosphate buffer, pH 7.2, 50 mM NaCl, 10mM TCEP/HCl, 1 mM DTE, 0.02% Na-azide, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 50 mM NaCl, 20 mM KPi / pH: 7.2 / Pressure: ambient / Temperature: 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeF.Delaglioprocessing
NMRView5.0.4B.A.Johnsondata analysis
X-PLOR-NIH2.9.9A.T.Bruenger, C.D.Schwietersstructure solution
X-PLOR-NIH2.9.9A.T.Bruenger, C.D.Schwietersrefinement
RefinementMethod: torsion angle dynamics, cartesian coordinate simulated annealing
Software ordinal: 1
Details: The structures are based on a total of 2592 NOE distance restraints, 163 dihedral angle restraints, 102 hydrogen bonds distance restraints, and 80 RDC restraints per monomer.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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