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- PDB-1bh8: HTAFII18/HTAFII28 HETERODIMER CRYSTAL STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1bh8
TitleHTAFII18/HTAFII28 HETERODIMER CRYSTAL STRUCTURE
Components
  • TAFII18
  • TAFII28
KeywordsTRANSCRIPTION REGULATION COMPLEX / HTAFII28 / HISTONE FOLD / TATA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation by host of viral transcription / nuclear vitamin D receptor binding / nuclear thyroid hormone receptor binding / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...positive regulation by host of viral transcription / nuclear vitamin D receptor binding / nuclear thyroid hormone receptor binding / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II transcribes snRNA genes / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription coactivator activity / protein heterodimerization activity / nucleolus / Golgi apparatus / DNA binding / nucleoplasm / nucleus
Similarity search - Function
TAFII28-like protein domain / Transcription initiation factor TFIID subunit 11-like / hTAFII28-like protein conserved region / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / Histone, subunit A / Histone, subunit A / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsBirck, C. / Poch, O. / Romier, C. / Ruff, M. / Mengus, G. / Lavigne, A.-C. / Davidson, I. / Moras, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Human TAF(II)28 and TAF(II)18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family.
Authors: Birck, C. / Poch, O. / Romier, C. / Ruff, M. / Mengus, G. / Lavigne, A.C. / Davidson, I. / Moras, D.
History
DepositionJun 16, 1998Processing site: BNL
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAFII18
B: TAFII28


Theoretical massNumber of molelcules
Total (without water)15,3882
Polymers15,3882
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-39 kcal/mol
Surface area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.400, 48.400, 77.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide TAFII18 / TRANSCRIPTION INITIATION FACTOR TFIID 18 KD SUBUNIT


Mass: 5266.026 Da / Num. of mol.: 1 / Fragment: RESIDUES 31 - 75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: HELA / Cellular location: NUCLEUSCell nucleus / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q15543
#2: Protein TAFII28 / TRANSCRIPTION INITIATION FACTOR TFIID 28 KD SUBUNIT


Mass: 10121.784 Da / Num. of mol.: 1 / Fragment: RESIDUES 113 - 201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: HELA / Cellular location: NUCLEUSCell nucleus / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q15544
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.9 / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-15 mg/mlprotein1drop
210 mMTris-HCl1drop
310 %PEG40001reservoir
4100 mMammonium sulfate1reservoir
5HEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9798
DetectorDetector: CCD / Date: Jan 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 3376 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 50 Å2 / Rsym value: 0.039 / Net I/σ(I): 21.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 12.8 / Rsym value: 0.115 / % possible all: 78.1
Reflection
*PLUS
Num. measured all: 9480 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 78.1 % / Rmerge(I) obs: 0.115

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.282 287 10 %RANDOM
Rwork0.199 ---
obs0.199 2924 84 %-
Displacement parametersBiso mean: 41.2 Å2
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 0 28 1102
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it2.492
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 3→3.1 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.315 28 10 %
Rwork0.223 229 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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