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- PDB-7lb3: Crystal structure of the second bromodomain (BD2) of human TAF1 b... -

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Basic information

Entry
Database: PDB / ID: 7lb3
TitleCrystal structure of the second bromodomain (BD2) of human TAF1 bound to ZS1-580
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


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-XXS / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKarim, M.R. / Schonbrunn, E.
CitationJournal: To Be Published
Title: Crystal structure of the second bromodomain (BD2) of human TAF1 bound to ZS1-580
Authors: Karim, M.R. / Schonbrunn, E.
History
DepositionJan 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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)16,3573
Polymers15,8831
Non-polymers4752
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint3 kcal/mol
Surface area8310 Å2
Unit cell
Length a, b, c (Å)46.755, 57.239, 59.069
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 / Fragment: second bromodomain
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
#2: Chemical ChemComp-XXS / 4-{4-[(3R)-3-methylmorpholin-4-yl]-6-[1-(S-methylsulfonimidoyl)cyclopropyl]pyrimidin-2-yl}-1H-indazole


Mass: 412.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N6O2S / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 293 K / Method: vapor diffusion, hanging drop / Details: 0.15 M MgCl2, 0.1 M Bis-Tris pH 5.5, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.9→41.11 Å / Num. obs: 13028 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 28.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.031 / Rrim(I) all: 0.082 / Net I/σ(I): 16.9 / Num. measured all: 89481
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.946.11.5150138210.6790.6581.6521.399.9
9.11-41.115.10.0357561490.9980.0170.03940.997

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHENIX1.19_4085refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JSP

7jsp


Resolution: 1.9→41.11 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 644 4.96 %
Rwork0.1885 12334 -
obs0.1895 12978 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.58 Å2 / Biso mean: 31.2116 Å2 / Biso min: 16.25 Å2
Refinement stepCycle: final / Resolution: 1.9→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 33 154 1301
Biso mean--23.24 37.22 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091173
X-RAY DIFFRACTIONf_angle_d1.2211596
X-RAY DIFFRACTIONf_dihedral_angle_d9.592154
X-RAY DIFFRACTIONf_chiral_restr0.065177
X-RAY DIFFRACTIONf_plane_restr0.008202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-2.050.36551270.320724232550
2.05-2.250.20671250.205924102535
2.25-2.580.22611300.200724502580
2.58-3.250.23021290.183124632592
3.25-41.110.16851330.16425882721
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)
13.29732.25652.13264.19332.26113.67860.1732-0.0021-0.21810.2992-0.0987-0.13480.51590.01-0.03960.18160.04570.01880.17830.01880.204314.66015.463259.7019
22.07131.39061.3383.11061.42352.65780.00990.02960.08080.0828-0.0498-0.00580.12690.00110.0550.12590.03390.02220.17560.01590.18178.636211.101760.41
37.42145.1106-6.28044.8345-2.96877.3261-0.07920.1996-0.00050.01140.36250.31630.6317-0.740.02920.4023-0.07180.00030.3075-0.03860.293-4.8101-12.332460.7282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1499 through 1539 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1540 through 1607 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1608 through 1635 )A0

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