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

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Basic information

Entry
Database: PDB / ID: 7jsp
TitleCrystal structure of the second bromodomain (BD2) of human TAF1 bound to ATR kinase inhibitor AZD6738
ComponentsTranscription initiation factor TFIID subunit 1
KeywordsGENE REGULATION / Bromodomain / TAF1 / non-BET / BET / kinase inhibitor / ATR / dual BRD-kinase
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 / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape ...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 / 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 / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 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 / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / negative regulation of ubiquitin-dependent protein catabolic process / 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 / 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 / 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, 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-VJM / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionAug 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 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)16,4554
Polymers15,8831
Non-polymers5733
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.670, 57.410, 59.000
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)
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-VJM / 4-(4-{1-[(R)-amino(hydroxy)methyl-lambda~4~-sulfanyl]cyclopropyl}-6-[(3R)-3-methylmorpholin-4-yl]pyrimidin-2-yl)-1H-pyrrolo[2,3-b]pyridine


Mass: 414.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N6O2S / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
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: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→21.7 Å / Num. obs: 17425 / % possible obs: 96.7 % / Redundancy: 4.951 % / Biso Wilson estimate: 29.695 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.022 / Rrim(I) all: 0.024 / Χ2: 0.992 / Net I/σ(I): 39.13 / Num. measured all: 86275 / Scaling rejects: 72
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
1.7-1.743.3380.2035.433812131211420.9740.24287
1.74-1.793.4040.1676.684017129811800.9820.19890.9
1.79-1.843.4350.1258.93968122711550.9870.14794.1
1.84-1.93.5040.10111.254033120011510.9930.11895.9
1.9-1.963.5310.07215.494022118011390.9960.08596.5
1.96-2.033.5840.05619.273899112010880.9970.06597.1
2.03-2.113.7780.04823.934152111810990.9970.05698.3
2.11-2.194.1080.03531.544202103510230.9990.0498.8
2.19-2.294.7340.03137.664777102510090.9990.03598.4
2.29-2.45.7150.02846.6154699729570.9990.03198.5
2.4-2.536.640.02854.15608292691610.0398.9
2.53-2.696.9890.02561.58614388787910.02799.1
2.69-2.876.9710.02366.0157798358290.9990.02599.3
2.87-3.16.9110.02271.65537778177810.02499.6
3.1-3.46.9990.0274.39495571370810.02299.3
3.4-3.86.90.01982.88454065865810.02100
3.8-4.396.7860.01685.08399058858810.018100
4.39-5.386.680.01786.21338050750610.01899.8
5.38-7.66.2580.0282.04250340040010.021100
7.6-21.75.3410.01876.43117524322010.0290.5

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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: 1.7→21.7 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 1097 6.3 %
Rwork0.1733 16319 -
obs0.1754 17416 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.11 Å2 / Biso mean: 37.9774 Å2 / Biso min: 14.48 Å2
Refinement stepCycle: final / Resolution: 1.7→21.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 69 117 1300
Biso mean--40.29 37.79 -
Num. residues----137
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.780.27441230.22641828195189
1.78-1.870.24071300.21881942207293
1.87-1.990.22721360.19662024216097
1.99-2.140.22011370.1892030216798
2.14-2.360.21261390.17882069220899
2.36-2.70.21281400.17422089222999
2.7-3.40.22471430.17382116225999
3.4-21.70.17061490.15312221237099
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)
12.34962.5780.70485.53340.49342.89710.02880.1426-0.2450.00320.0016-0.04440.55230.1494-0.01030.2140.05110.01290.198-0.03640.221812.62681.683255.375
27.54060.54440.46264.4215-0.39784.0913-0.033-0.41810.4260.4761-0.01130.0958-0.19090.20550.0460.2125-0.0037-0.00750.19710.00680.171715.196715.801471.1121
33.41461.66350.91915.40620.89062.35730.0246-0.01550.09090.2076-0.01040.14040.1792-0.0444-0.02370.14330.02420.02350.15110.00070.09017.62768.972862.1108
44.43835.37143.972310.04055.3835.0013-0.18430.5016-0.0147-0.240.3583-0.13670.05770.4286-0.16770.18790.0158-0.00060.30570.02470.18189.058412.878951.4986
56.96295.4215-7.54424.6275-4.64168.5984-0.08820.31510.1487-0.00370.3507-0.0110.1969-0.8001-0.08340.4076-0.1150.04370.2975-0.03250.2703-4.6446-12.336960.5659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1499 through 1528 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1529 through 1549 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1550 through 1587 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1588 through 1607 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1608 through 1635 )A0

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