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- PDB-7k03: Crystal structure of the tandem bromodomain (BD1 and BD2) of huma... -

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Basic information

Entry
Database: PDB / ID: 7k03
TitleCrystal structure of the tandem bromodomain (BD1 and BD2) of human TAF1 bound to ATR kinase inhibitor AZD6738
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 / peptidyl-threonine phosphorylation / transcription initiation at RNA polymerase II promoter / 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 / peptidyl-serine phosphorylation / ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / sequence-specific DNA binding / protein autophosphorylation / transcription by RNA polymerase II / non-specific serine/threonine protein kinase / protein stabilization / 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-VJM / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / 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
DepositionSep 3, 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)31,6316
Polymers30,9681
Non-polymers6635
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.500, 54.320, 122.710
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) / 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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate, 20% Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 27, 2017 / Details: RIGAKU SATURN 944+
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→40.67 Å / Num. obs: 40469 / % possible obs: 98.7 % / Redundancy: 9.104 % / Biso Wilson estimate: 22.897 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.041 / Χ2: 1.009 / Net I/σ(I): 34.33 / Num. measured all: 368444 / Scaling rejects: 429
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
1.6-1.644.850.4563.2212779297526350.8430.50688.6
1.64-1.695.4970.3564.4615369294227960.9080.39195
1.69-1.745.9930.2945.6916786280428010.9420.32199.9
1.74-1.796.3590.2467.1817323274827240.9680.26799.1
1.79-1.856.5880.2078.8917525266026600.9740.224100
1.85-1.916.7750.15212.1717690261226110.9880.165100
1.91-1.986.9330.11515.917305249624960.9920.124100
1.98-2.077.2970.08921.0317636241824170.9960.096100
2.07-2.168.0090.06927.7118636232923270.9980.07499.9
2.16-2.269.3060.05635.4120567221022100.9980.06100
2.26-2.3911.4120.04944.6524034210621060.9990.052100
2.39-2.5313.4990.04753.0327349202620260.9990.049100
2.53-2.714.0190.04259.0926299187618760.9990.044100
2.7-2.9213.9890.03766.11245651756175610.038100
2.92-3.213.9630.03175.49231081655165510.032100
3.2-3.5813.9330.02685.29204821470147010.027100
3.58-4.1313.6990.02395.96184111344134410.024100
4.13-5.0613.4520.02197.8153491141114110.022100
5.06-7.1613.0430.02587.11159588988910.026100
7.16-40.6710.6540.02289.64563654152910.02397.8

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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: PDBID 7JJH

7jjh


Resolution: 1.6→40.67 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1805 1012 2.5 %
Rwork0.1523 39442 -
obs0.153 40454 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.94 Å2 / Biso mean: 22.5989 Å2 / Biso min: 8.23 Å2
Refinement stepCycle: final / Resolution: 1.6→40.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 103 359 2480
Biso mean--24.82 31.46 -
Num. residues----248
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 (%)
1.6-1.680.21351320.18735163529592
1.68-1.790.20511430.17295564570799
1.79-1.930.18991450.164956505795100
1.93-2.120.18381450.151856505795100
2.12-2.430.15971460.141657005846100
2.43-3.060.19011470.148257585905100
3.06-40.670.17241540.147959576111100
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)
11.31370.3012-0.95291.276-0.27212.65680.0118-0.11130.2370.11750.0257-0.0111-0.1366-0.0987-0.09890.10830.0079-0.00470.0973-0.03080.1319-128.8048-145.9285133.6012
21.4244-0.1651-1.00151.8242-0.20794.11410.0502-0.02280.12810.14870.07850.0434-0.0557-0.49090.03810.06820.00910.00670.13480.00310.1036-134.4907-150.2543129.3886
32.70640.104-2.32091.53220.71115.3606-0.23170.0385-0.12340.11940.0376-0.06580.2927-0.14740.18660.09970.00360.00790.0716-0.00580.1094-126.1372-156.7644128.65
42.63530.5274-2.53791.4278-0.56255.9951-0.0901-0.3656-0.11330.1628-0.0349-0.1550.06080.3665-0.00120.12430.0213-0.0170.15860.00480.1262-119.8233-153.6469136.0286
50.61220.7943-0.02062.04550.9190.82210.1624-0.2232-0.0870.4121-0.0824-0.09390.0993-0.0072-0.0390.1812-0.0143-0.02330.20670.03730.0967-136.3578-167.7173146.1126
61.45330.4827-0.58962.1347-0.60671.7178-0.0380.0015-0.0477-0.0732-0.0468-0.0639-0.05960.05550.02180.08090.0067-0.00410.0879-0.02330.1268-133.7758-170.4524119.9771
71.4690.2105-0.7880.94690.22424.24540.0288-0.1142-0.03790.0654-0.03220.0301-0.1424-0.12980.0110.0928-0.0028-0.00050.0852-0.00590.1128-141.2992-171.7973129.3358
81.90451.1658-1.8271.4386-1.1676.2345-0.10360.0476-0.3264-0.0595-0.0013-0.12430.22560.08730.20640.10860.00630.01760.0874-0.01420.1806-140.1863-183.3444123.2206
91.29381.15811.06554.884-0.55571.7117-0.1028-0.22780.00580.6944-0.0490.25830.2463-0.33670.14840.2456-0.04510.0030.2620.02890.1337-148.2402-176.9007146.5329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1378 through 1416 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1417 through 1441 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1442 through 1464 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1465 through 1483 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1484 through 1517 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1518 through 1549 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1550 through 1583 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1584 through 1606 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1607 through 1625 )A0

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