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- PDB-6bqd: TAF1-BD2 bromodomain in complex with (E)-3-(6-(but-2-en-1-yl)-7-o... -

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Basic information

Entry
Database: PDB / ID: 6bqd
TitleTAF1-BD2 bromodomain in complex with (E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide
ComponentsTranscription initiation factor TFIID subunit 1
KeywordsGENE REGULATION / TAF1-BD2 / Bromodomain
Function / homology
Function and homology information


negative regulation of protein autoubiquitination / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / positive regulation of androgen receptor activity / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / cellular response to ATP / midbrain development / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex ...negative regulation of protein autoubiquitination / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / positive regulation of androgen receptor activity / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / cellular response to ATP / midbrain development / 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 / ubiquitin conjugating enzyme activity / MLL1 complex / transcription initiation at RNA polymerase I promoter / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / negative regulation of ubiquitin-dependent protein catabolic process / 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 / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / positive regulation of protein binding / kinase activity / ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / 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 / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / cell cycle / protein heterodimerization activity / negative regulation of gene expression / protein phosphorylation / 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
Chem-69G / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.136 Å
AuthorsMurray, J.M. / Tang, Y.
CitationJournal: J. Comput. Aided Mol. Des. / Year: 2019
Title: Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison.
Authors: Nittinger, E. / Gibbons, P. / Eigenbrot, C. / Davies, D.R. / Maurer, B. / Yu, C.L. / Kiefer, J.R. / Kuglstatter, A. / Murray, J. / Ortwine, D.F. / Tang, Y. / Tsui, V.
History
DepositionNov 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 1
B: Transcription initiation factor TFIID subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8854
Polymers30,2142
Non-polymers6712
Water97354
1
A: Transcription initiation factor TFIID subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4422
Polymers15,1071
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcription initiation factor TFIID subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4422
Polymers15,1071
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.553, 42.510, 63.372
Angle α, β, γ (deg.)90.000, 103.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcription initiation factor TFIID subunit 1 / Cell cycle gene 1 protein / TBP-associated factor 250 kDa / p250 / Transcription initiation factor ...Cell cycle gene 1 protein / TBP-associated factor 250 kDa / p250 / Transcription initiation factor TFIID 250 kDa subunit / TAFII250


Mass: 15106.939 Da / Num. of mol.: 2 / Fragment: TAF1-BD2 bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Production host: Escherichia coli (E. coli)
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-69G / 3-{6-[(2E)-but-2-en-1-yl]-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl}-N,N-dimethylbenzamide


Mass: 335.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21N3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5 / Details: 8% Tacsimate pH 5.0 and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.136→39.558 Å / Num. obs: 18311 / % possible obs: 97.55 % / Redundancy: 3 % / Biso Wilson estimate: 40.35 Å2 / Net I/σ(I): 12
Reflection shellResolution: 2.1364→2.249 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_2747refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 5I29

5i29


Resolution: 2.136→39.558 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.11
RfactorNum. reflection% reflection
Rfree0.2264 945 5.16 %
Rwork0.1851 --
obs0.1872 18311 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.23 Å2 / Biso mean: 50.2059 Å2 / Biso min: 28.93 Å2
Refinement stepCycle: final / Resolution: 2.136→39.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 51 54 2210
Biso mean--41.48 44.03 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122205
X-RAY DIFFRACTIONf_angle_d1.0772997
X-RAY DIFFRACTIONf_chiral_restr0.063328
X-RAY DIFFRACTIONf_plane_restr0.007392
X-RAY DIFFRACTIONf_dihedral_angle_d17.9741323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1364-2.2490.29761090.25822260236989
2.249-2.38990.27951340.22772467260199
2.3899-2.57440.27851350.21082490262599
2.5744-2.83340.22241580.20322497265598
2.8334-3.24320.24851350.21422511264699
3.2432-4.08540.23381420.18132520266299
4.0854-39.5650.18481320.15092621275399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9330.77140.02371.8663-0.03061.43990.0270.1031-0.12970.2282-0.1766-0.0613-0.06050.3959-0.00050.3594-0.0647-0.04060.37750.04970.270916.9972.97679.555
21.5475-0.0104-0.14870.98210.11540.574-0.03830.4473-0.21950.0131-0.10820.18480.0934-0.1343-0.00380.307-0.02840.0260.3785-0.10860.38810.169-11.85967.409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1501:1629 )A1501 - 1629
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1502:1630 )B1502 - 1630

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