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- PDB-7k0d: Crystal structure of the tandem bromodomain (BD1, BD2) of human T... -

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Basic information

Entry
Database: PDB / ID: 7k0d
TitleCrystal structure of the tandem bromodomain (BD1, BD2) of human TAF1 bound to mTORC1/2 inhibitor AZD3147
ComponentsTranscription initiation factor TFIID subunit 1
KeywordsGENE REGULATION / TAF1 / non-BET / BET / kinase inhibitor / ATR / dual BRD-kinase / transferase
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 / midbrain development / cellular response to ATP / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity ...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 / midbrain development / cellular response to ATP / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor 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 / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of ubiquitin-dependent protein catabolic process / histone 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 / positive regulation of protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / kinase activity / ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / transcription by RNA polymerase II / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-VQS / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionSep 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
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
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)31,4862
Polymers30,9681
Non-polymers5181
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.290, 72.380, 77.110
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: 30968.256 Da / Num. of mol.: 1 / Fragment: TANDEM BROMODOMAINS, RESIDUES 1373-1635
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-VQS / N-(4-{4-[1-(cyclopropylsulfonyl)cyclopropyl]-6-[(3S)-3-methylmorpholin-4-yl]pyrimidin-2-yl}phenyl)-N'-(2-hydroxyethyl)thiourea


Mass: 517.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H31N5O4S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M MES monohydrate, 30% Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→36.02 Å / Num. obs: 14496 / % possible obs: 99.6 % / Redundancy: 7.343 % / Biso Wilson estimate: 70.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.042 / Χ2: 1.033 / Net I/σ(I): 22.82
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
2.25-2.317.7650.6982.8674549639600.9330.74899.7
2.31-2.377.8110.5673.4874449599530.9350.60799.4
2.37-2.447.7620.4264.5172119329290.9580.45799.7
2.44-2.527.6420.3265.6569319139070.9770.3599.3
2.52-2.67.6010.2188.0967658908900.990.234100
2.6-2.697.5670.179.7763798478430.9950.18399.5
2.69-2.797.4280.13412.561138268230.9950.14499.6
2.79-2.97.2550.10315.4858408068050.9960.11199.9
2.9-3.037.0760.07919.8553147527510.9980.08699.9
3.03-3.186.2290.06323.4345667387330.9970.06899.3
3.18-3.357.5210.05431.452426986970.9990.05899.9
3.35-3.567.6240.04239.3251316746730.9990.04599.9
3.56-3.87.4980.03744.0647916396390.9990.04100
3.8-4.117.3580.03348.1742315755750.9990.036100
4.11-4.57.3090.03150.3939695475430.9990.03399.3
4.5-5.037.0630.0351.734824934930.9990.032100
5.03-5.816.4760.0348.8328434414390.9990.03299.5
5.81-7.126.3270.03248.6824173853820.9990.03499.2
7.12-10.066.9640.02855.3621173053040.9990.0399.7
10.06-36.025.6690.02950.1810091841780.9990.03196.7

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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: PDB ID 7K03

7k03


Resolution: 2.2→36.02 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 725 5 %
Rwork0.2297 13771 -
obs0.2308 14496 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.61 Å2 / Biso mean: 87.3031 Å2 / Biso min: 51.32 Å2
Refinement stepCycle: final / Resolution: 2.2→36.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 35 9 2014
Biso mean--85.2 73.63 -
Num. residues----250
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.25-2.370.39131420.33822694
2.37-2.610.35471430.3012713
2.61-2.990.38181430.29142725
2.99-3.760.2611450.25962753
3.76-36.020.21261520.19592886
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)
13.19460.18380.21042.9642.42158.2188-0.3463-0.0149-0.0714-0.3101-0.0894-0.0566-0.56140.09830.3580.43770.0113-0.01610.48460.01380.5221-6.4557-17.24683.631
25.3392-3.51141.64326.0837-2.65915.52630.53640.30390.0046-1.0987-0.2241-0.2470.55330.5853-0.26010.7725-0.02680.00360.6653-0.07710.54-0.7741-42.8946-4.8104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1379 through 1501 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1502 through 1628 )A0

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