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- PDB-1eqf: CRYSTAL STRUCTURE OF THE DOUBLE BROMODOMAIN MODULE FROM HUMAN TAFII250 -

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Basic information

Entry
Database: PDB / ID: 1eqf
TitleCRYSTAL STRUCTURE OF THE DOUBLE BROMODOMAIN MODULE FROM HUMAN TAFII250
ComponentsRNA POLYMERASE II TRANSCRIPTION INITIATION FACTOR
KeywordsTRANSCRIPTION / Four-Helix Bundle / Acetylated Histone-Tail Binding Protein
Function / homology
Function and homology information


negative regulation of protein autoubiquitination / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition / positive regulation of androgen receptor activity / RNA polymerase II general transcription initiation factor binding / cellular response to ATP / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / transcription regulator inhibitor activity / midbrain development ...negative regulation of protein autoubiquitination / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition / positive regulation of androgen receptor activity / RNA polymerase II general transcription initiation factor binding / cellular response to ATP / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / transcription regulator inhibitor activity / midbrain development / histone acetyltransferase activity / 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 / ubiquitin conjugating enzyme activity / transcription initiation at RNA polymerase I promoter / MLL1 complex / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / regulation of signal transduction by p53 class mediator / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / lysine-acetylated histone binding / mRNA transcription by RNA polymerase II / protein polyubiquitination / cellular response to UV / p53 binding / kinase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of protein binding / peptidyl-serine phosphorylation / ubiquitin-dependent protein catabolic process / protein autophosphorylation / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein stabilization / protein phosphorylation / protein heterodimerization activity / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus
Similarity search - Function
TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / Bromodomain-like ...TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsJacobson, R.H. / Ladurner, A.G. / King, D.S. / Tjian, R.
CitationJournal: Science / Year: 2000
Title: Structure and function of a human TAFII250 double bromodomain module.
Authors: Jacobson, R.H. / Ladurner, A.G. / King, D.S. / Tjian, R.
History
DepositionApr 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA POLYMERASE II TRANSCRIPTION INITIATION FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8022
Polymers32,7061
Non-polymers961
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.100, 58.100, 101.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein RNA POLYMERASE II TRANSCRIPTION INITIATION FACTOR / TAFII250


Mass: 32706.221 Da / Num. of mol.: 1 / Fragment: DOUBLE BROMODOMAIN, RESIDUES 1359-1638
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P21675
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: ammonium sulfate, TrisCl, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
21.4 Mammonium sulfate11
3100 mMTris-HCl11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9801
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.1→51.3 Å / Num. all: 17504 / Num. obs: 17084 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 17.3
Reflection shellResolution: 2.1→29.1 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.341 / Num. unique all: 2711 / % possible all: 97.6
Reflection
*PLUS
Num. measured all: 122732
Reflection shell
*PLUS
% possible obs: 97.6 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.1→29.1 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1635 -Random
Rwork0.218 ---
all0.246 16102 --
obs0.218 14467 93.5 %-
Refinement stepCycle: LAST / Resolution: 2.1→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 5 161 2358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.14

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