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- PDB-5igl: Crystal structure of the second bromodomain of human TAF1L in com... -

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Basic information

Entry
Database: PDB / ID: 5igl
TitleCrystal structure of the second bromodomain of human TAF1L in complex with bromosporine (BSP)
ComponentsTranscription initiation factor TFIID subunit 1-like
KeywordsTRANSCRIPTION / TAF1/TAFII250 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


male meiotic nuclear division / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 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 ...male meiotic nuclear division / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 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 / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / : / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / Regulation of TP53 Activity through Phosphorylation / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm
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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromosporine / Transcription initiation factor TFIID subunit 1-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Felletar, I. / Krojer, T. / Tallant, C. / von Delft, F. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Sci Adv / Year: 2016
Title: Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia.
Authors: Picaud, S. / Leonards, K. / Lambert, J.P. / Dovey, O. / Wells, C. / Fedorov, O. / Monteiro, O. / Fujisawa, T. / Wang, C.Y. / Lingard, H. / Tallant, C. / Nikbin, N. / Guetzoyan, L. / Ingham, ...Authors: Picaud, S. / Leonards, K. / Lambert, J.P. / Dovey, O. / Wells, C. / Fedorov, O. / Monteiro, O. / Fujisawa, T. / Wang, C.Y. / Lingard, H. / Tallant, C. / Nikbin, N. / Guetzoyan, L. / Ingham, R. / Ley, S.V. / Brennan, P. / Muller, S. / Samsonova, A. / Gingras, A.C. / Schwaller, J. / Vassiliou, G. / Knapp, S. / Filippakopoulos, P.
History
DepositionFeb 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,4282
Polymers18,0231
Non-polymers4041
Water45025
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.172, 89.177, 117.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-1815-

HOH

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Components

#1: Protein Transcription initiation factor TFIID subunit 1-like / TAF(II)210 / TBP-associated factor 1-like / TBP-associated factor 210 kDa / Transcription ...TAF(II)210 / TBP-associated factor 1-like / TBP-associated factor 210 kDa / Transcription initiation factor TFIID 210 kDa subunit


Mass: 18023.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1L / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IZX4
#2: Chemical ChemComp-BMF / Bromosporine / ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3-b]pyridazin-8-yl)carbamate


Mass: 404.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N6O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
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: 3.22 Å3/Da / Density % sol: 61.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 63%(v/v) MPD, 0.1M MMT pH 7.5 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→44.46 Å / Num. obs: 13934 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.022 / Net I/av σ(I): 16.6 / Net I/σ(I): 16.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

2grc

2nxb

2oo1

2oss

2ouo

2rfj

3dai

3d7c

3dwy


Resolution: 2.1→44.46 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 19.079 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29418 695 5 %RANDOM
Rwork0.2112 ---
obs0.21484 13238 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.071 Å2
Baniso -1Baniso -2Baniso -3
1-7.67 Å20 Å2-0 Å2
2---1.83 Å20 Å2
3----5.84 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 28 25 1148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021150
X-RAY DIFFRACTIONr_bond_other_d0.0030.021048
X-RAY DIFFRACTIONr_angle_refined_deg2.3371.9691570
X-RAY DIFFRACTIONr_angle_other_deg1.2993.0072401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5195138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.64125.57752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.84615182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.344152
X-RAY DIFFRACTIONr_chiral_restr0.1530.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211307
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02262
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it13.6868.938555
X-RAY DIFFRACTIONr_mcbond_other13.7018.916554
X-RAY DIFFRACTIONr_mcangle_it16.47516.658694
X-RAY DIFFRACTIONr_mcangle_other16.4716.651693
X-RAY DIFFRACTIONr_scbond_it19.05410.487594
X-RAY DIFFRACTIONr_scbond_other19.03810.487595
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other21.54818.603877
X-RAY DIFFRACTIONr_long_range_B_refined21.14352.0961345
X-RAY DIFFRACTIONr_long_range_B_other21.16152.0921345
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 60 -
Rwork0.419 937 -
obs--99.6 %
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)
10.0216-0.1190.14481.34780.09634.5084-0.0338-0.0085-0.02810.0096-0.02680.0117-0.2651-0.29850.06060.1315-0.00520.03530.05540.00830.19628.720234.161846.2618
20.1380.45140.07811.55030.25381.8351-0.1460.0563-0.0259-0.29540.1755-0.0801-0.33360.1958-0.02960.4633-0.0797-0.00490.04140.00410.07197.827736.474535.9441
30.2167-0.8105-0.490421.035815.542811.5865-0.3072-0.01110.1166-0.05340.03920.4212-0.270.05810.26790.5706-0.0263-0.06160.0251-0.09720.44776.153262.310961.6955
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1512 - 1556
2X-RAY DIFFRACTION2A1557 - 1628
3X-RAY DIFFRACTION3A1629 - 1650

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