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- PDB-7jjg: Crystal structure of the second bromodomain (BD2) of human TAF1 b... -

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Basic information

Entry
Database: PDB / ID: 7jjg
TitleCrystal structure of the second bromodomain (BD2) of human TAF1 bound to ATR kinase inhibitor AZ20
ComponentsTranscription initiation factor TFIID subunit 1
KeywordsGENE REGULATION / Bromodomain / TAF1 / non-BET / BET / kinase inhibitor / ATR / dual BRD-kinase / transferase-transferase inhibitor complex
Function / homology
Function and homology information


positive regulation of androgen receptor signaling pathway / negative regulation of protein autoubiquitination / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition / histone H4K16ac reader activity / RNA polymerase II general transcription initiation factor binding / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape ...positive regulation of androgen receptor signaling pathway / negative regulation of protein autoubiquitination / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition / histone H4K16ac reader activity / RNA polymerase II general transcription initiation factor 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 / midbrain development / cellular response to ATP / negative regulation of signal transduction by p53 class mediator / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / MLL1 complex / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase activity / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / transcription regulator inhibitor activity / 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 / mRNA transcription by RNA polymerase II / protein polyubiquitination / p53 binding / cellular response to UV / kinase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein autophosphorylation / ubiquitin-dependent protein catabolic process / transcription regulator complex / Regulation of TP53 Activity through Phosphorylation / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / non-specific serine/threonine protein kinase / protein kinase activity / protein stabilization / 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, conserved site ...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, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-VCD / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKarim, M.R. / Schonbrunn, E.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of Dual TAF1-ATR Inhibitors and Ligand-Induced Structural Changes of the TAF1 Tandem Bromodomain.
Authors: Karim, R.M. / Yang, L. / Chen, L. / Bikowitz, M.J. / Lu, J. / Grassie, D. / Shultz, Z.P. / Lopchuk, J.M. / Chen, J. / Schonbrunn, E.
History
DepositionJul 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,4494
Polymers15,8831
Non-polymers5673
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.740, 57.470, 59.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 15882.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Plasmid: pNIC28.Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-VCD / 4-{4-[(3R)-3-methylmorpholin-4-yl]-6-[1-(methylsulfonyl)cyclopropyl]pyrimidin-2-yl}-1H-indole


Mass: 412.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Co(II) chloride, 0.1 M Sodium acetate trihydrate (pH 4.6), 1 M 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→36.71 Å / Num. obs: 21689 / % possible obs: 99.9 % / Redundancy: 7.176 % / Biso Wilson estimate: 28.449 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Χ2: 1.008 / Net I/σ(I): 25.48 / Num. measured all: 155631 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.647.2360.7812.4911484158815870.7710.84299.9
1.64-1.697.2380.5983.2411059152815280.8680.645100
1.69-1.747.2660.4933.9410906150215010.8980.53199.9
1.74-1.797.2830.3795.1710539144914470.9540.40899.9
1.79-1.857.2520.282710204140814070.9630.30499.9
1.85-1.917.2730.2178.959971137213710.9820.23499.9
1.91-1.987.2870.14912.829626132013210.9920.16100
1.98-2.077.2690.10717.89290127912780.9960.11599.9
2.07-2.167.2670.08321.888887122312230.9970.09100
2.16-2.267.2710.06627.838500116911690.9980.071100
2.26-2.397.2320.05332.238150112811270.9990.05799.9
2.39-2.537.2360.046377562104510450.9990.049100
2.53-2.77.1690.0442.047291101810170.9990.04399.9
2.7-2.927.0950.03448.3565709289260.9990.03699.8
2.92-3.27.0250.02955.2660918678670.9990.031100
3.2-3.586.9790.02564.52555579779610.02799.9
3.58-4.136.8610.02271.5248517077070.9990.024100
4.13-5.066.8710.01872.12414360360310.019100
5.06-7.166.7080.01969.07319347647610.02100
7.16-36.716.0030.01969.8217592952930.9990.02199.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UV4

3uv4


Resolution: 1.6→36.71 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 1085 5 %
Rwork0.1688 20603 -
obs0.1701 21688 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.71 Å2 / Biso mean: 26.1453 Å2 / Biso min: 11.6 Å2
Refinement stepCycle: final / Resolution: 1.6→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 77 155 1346
Biso mean--26.76 33.16 -
Num. residues----137
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.670.23311330.206225252658
1.67-1.760.2131330.190125302663
1.76-1.870.21031340.181125352669
1.87-2.020.22131340.17125482682
2.02-2.220.18691350.15925682703
2.22-2.540.18631350.156125632698
2.54-3.20.18561370.168526022739
3.2-36.710.19241440.168427322876

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