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- PDB-7jjh: Crystal structure of the unliganded tandem bromodomain (BD1, BD2)... -

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Basic information

Entry
Database: PDB / ID: 7jjh
TitleCrystal structure of the unliganded tandem bromodomain (BD1, BD2) of human TAF1
ComponentsTranscription initiation factor TFIID subunit 1
KeywordsGENE REGULATION / Bromodomain / TAF1 / non-BET / BET / kinase inhibitor / ATR / dual BRD-kinase / transferase
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 / midbrain development / HIV Transcription Initiation ...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 / 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 / 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 / transcription regulator inhibitor activity / 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 / mRNA transcription by RNA polymerase II / protein polyubiquitination / cellular response to UV / p53 binding / 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
Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.0Jan 27, 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,4038
Polymers30,9681
Non-polymers4347
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.690, 199.720, 88.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1857-

HOH

21A-1947-

HOH

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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
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): RIPL
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 4.24 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.8 M Succinic Acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.1→19.49 Å / Num. obs: 28879 / % possible obs: 96.4 % / Redundancy: 14.739 % / Biso Wilson estimate: 37.222 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.076 / Χ2: 1.005 / Net I/σ(I): 27.46 / Num. measured all: 425655 / Scaling rejects: 220
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
2.1-2.1514.550.4147.8529813217220490.9380.42994.3
2.15-2.2115.040.3858.630426213920230.9680.39894.6
2.21-2.2815.0610.32310.2429595207719650.9760.33494.6
2.28-2.3515.0780.31110.2829010201719240.9810.32295.4
2.35-2.4215.0250.26811.7727676192318420.9860.27895.8
2.42-2.5115.0750.26111.9427572190618290.9870.2796
2.51-2.614.9670.21713.7226238182717530.9930.22495.9
2.6-2.7115.0060.16916.8125631177217080.9960.17596.4
2.71-2.8314.9660.13920.1724544169516400.9970.14496.8
2.83-2.9714.9020.11923.4123501162515770.9980.12397
2.97-3.1314.8050.0930.4122192153814990.9980.09397.5
3.13-3.3214.7780.07634.2121132146414300.9990.07997.7
3.32-3.5514.6610.05445.3219836138513530.9990.05697.7
3.55-3.8314.5080.04353.8618396128612680.9990.04598.6
3.83-4.214.4860.03860.3170361198117610.03998.2
4.2-4.714.2290.03466.5715339109610780.9990.03698.4
4.7-5.4214.2170.03564.92135209589510.9990.03699.3
5.42-6.6413.9340.03761.17114828308240.9990.03999.3
6.64-9.3913.4220.02774.23881866065710.02899.5
9.39-19.4911.7060.02676.6638983933330.9980.02784.7

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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: 3UV5

3uv5


Resolution: 2.1→19.49 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 1010 3.5 %
Rwork0.1875 27865 -
obs0.1886 28875 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.75 Å2 / Biso mean: 46.8533 Å2 / Biso min: 17.64 Å2
Refinement stepCycle: final / Resolution: 2.1→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 32 229 2329
Biso mean--56.6 49.91 -
Num. residues----253
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 (%)
2.1-2.210.2521380.25073825396394
2.21-2.350.24481410.21463881402295
2.35-2.530.23741410.20623903404496
2.53-2.780.24771430.21323941408496
2.78-3.180.26211450.20713999414497
3.19-4.010.23531470.18174062420998
4.01-19.490.1691550.15294254440999
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)
13.2778-0.10490.28844.05192.22994.5141-0.15870.28390.0333-0.2298-0.0110.04360.4430.47450.16440.52870.03680.0120.2494-0.00020.303553.3242211.3581-0.0165
23.25422.37952.26826.49535.12676.954-0.20440.24780.4261-0.6171-0.32610.8159-0.4733-0.07860.540.46880.055-0.10710.30040.01520.365845.0099218.9026-0.7835
34.21570.7694-2.13890.9235-0.37532.5826-0.0502-0.0447-0.2040.0431-0.064-0.11920.12420.35380.08380.14450.0439-0.010.33470.03720.247471.8167245.82368.6251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1378 through 1441 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1442 through 1501 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1502 through 1630 )A0

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