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- PDB-6p39: Crystal Structure Analysis of TAF1 Bromodomain -

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Basic information

Entry
Database: PDB / ID: 6p39
TitleCrystal Structure Analysis of TAF1 Bromodomain
ComponentsTranscription initiation factor TFIID subunit 1
KeywordsTRANSFERASE / kinase / bromodomain / inhibitor / TRANSCRIPTION
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 / transcription factor TFIID complex / MLL1 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 / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of protein binding / kinase activity / ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / cell cycle / 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-like ...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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-NQY / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.941 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of TAF1 Bromodomain
Authors: Seo, H.-S. / Dhe-Paganon, S.
History
DepositionMay 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,4762
Polymers15,9981
Non-polymers4791
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.600, 96.600, 91.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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: 15997.900 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 / Production host: Escherichia coli (E. coli)
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NQY / 3-methoxy-4-{[(6aR)-5-methyl-6-oxo-6,6a,7,8,9,10-hexahydro-5H-dipyrido[1,2-a:3',2'-e]pyrazin-2-yl]amino}-N-(1-methylpiperidin-4-yl)benzamide


Mass: 478.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H34N6O3 / Feature type: SUBJECT OF INVESTIGATION

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG1000, Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.94→45.56 Å / Num. obs: 10784 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 80.951 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.092 / Net I/σ(I): 15.8 / Num. measured all: 104018
Reflection shellResolution: 2.94→2.99 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.4 / Num. measured all: 5346 / Num. unique obs: 521 / Rpim(I) all: 0.599 / Rrim(I) all: 1.928 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UV5

3uv5


Resolution: 2.941→42.676 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.67
RfactorNum. reflection% reflection
Rfree0.2123 536 4.98 %
Rwork0.1926 --
obs0.1936 10763 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 192.39 Å2 / Biso mean: 99.8515 Å2 / Biso min: 60.85 Å2
Refinement stepCycle: final / Resolution: 2.941→42.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 35 0 1080
Biso mean--129.62 --
Num. residues----128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9405-3.23630.32571320.330525202652
3.2363-3.70440.30831240.257325232647
3.7044-4.66620.2011200.185225572677
4.6662-42.68080.18381600.158826272787
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)
19.26321.71824.16095.73591.64874.5521-0.57880.3401-0.9881-1.04590.8785-0.1493-0.95790.6193-0.35920.7166-0.21320.08170.90410.05660.820340.3735-38.9077-31.2615
22.4131-3.72862.39217.6826-3.25817.0519-0.01960.13320.38741.0008-0.2932-1.3758-1.04721.5322-0.33230.9103-0.0646-0.07420.9504-0.0950.923547.2045-30.0661-15.252
37.06641.42442.24944.82881.01843.51890.23620.6572-0.23150.67260.0980.38080.29640.3888-0.81610.92530.03180.00360.9565-0.03270.915755.2322-41.046-7.2119
49.2352-3.092-1.94043.5175-1.98133.1874-0.39040.9687-1.0048-0.30370.3623-1.026-0.04591.2158-0.26480.8018-0.0659-0.0031.0451-0.16570.93848.9873-40.1245-23.022
56.16741.68063.79292.22182.83148.87330.1222-0.7969-0.07520.3276-0.29340.25010.4205-0.75380.18960.82730.01220.07520.97440.01920.924640.0547-38.3312-13.641
64.91010.25652.92362.51431.1842.56950.14960.4531-1.36610.32660.01540.33120.46250.28960.20691.003-0.06890.07041.0818-0.03371.110431.8862-48.0465-32.5683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1521 through 1538 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1539 through 1552 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1553 through 1570 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1571 through 1579 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1580 through 1627 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1628 through 1648 )A0

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