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- PDB-3uv5: Crystal Structure of the tandem bromodomains of human Transcripti... -

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Basic information

Entry
Database: PDB / ID: 3uv5
TitleCrystal Structure of the tandem bromodomains of human Transcription initiation factor TFIID subunit 1 (TAF1)
ComponentsTranscription initiation factor TFIID subunit 1
KeywordsTRANSCRIPTION / Tandem bromodomain / TAF1 / Cell cycle gene 1 protein / TBP-associated factor 250 kDa / Transcription initiation factor TFIID 250 kDa subunit / TFII-250 / Structural Genomics Consortium / SGC
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-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
Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsFilippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Muniz, J. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Filippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Muniz, J. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionNov 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)31,0902
Polymers30,9681
Non-polymers1221
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.760, 199.990, 88.020
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-150-

HOH

21A-225-

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 / TAF(II)250 / TAFII-250 / TAFII250


Mass: 30968.256 Da / Num. of mol.: 1 / Fragment: unp residues 1373-1635
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BA2R, CCG1, CCGS, TAF1, TAF2A / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: P21675, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 4.1 Å3/Da / Density meas: 70.03 Mg/m3 / Density % sol: 70.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1M Tris-HCl, 1.1M (NH4)2SO4, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionRedundancy: 6.5 % / Av σ(I) over netI: 6 / Number: 216346 / Rsym value: 0.092 / D res high: 2.03 Å / D res low: 34.482 Å / Num. obs: 33176 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.4234.4897.410.0390.0396.4
4.546.4299.910.0750.0756.1
3.714.5410010.0620.0626.8
3.213.7110010.070.077
2.873.2110010.0940.0947
2.622.8710010.130.137.1
2.432.6210010.2080.2087.2
2.272.4310010.3090.3097.2
2.142.2799.810.4580.4586.4
2.032.1495.110.7410.7414.4
ReflectionResolution: 2.03→34.482 Å / Num. all: 33444 / Num. obs: 33176 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 35.7 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.03-2.144.40.74112041145870.74195.1
2.14-2.276.40.4581.62890445430.45899.8
2.27-2.437.20.3092.53082742960.309100
2.43-2.627.20.2083.72876240140.208100
2.62-2.877.10.135.72630436980.13100
2.87-3.2170.0947.42367033630.094100
3.21-3.7170.079.32079729920.07100
3.71-4.546.80.0629.91729425480.062100
4.54-6.426.10.07581213419960.07599.9
6.42-34.4826.40.03915.1724311390.03997.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.69 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.48 Å
Translation2.5 Å34.48 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
GDAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of PDB entries 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3DAI, 3D7C, 3DWY, 3G0L, 3GG3

3hmh

2grc

2oo1

2oss

2ouo

3dai

3d7c

3dwy

3g0l

3gg3


Resolution: 2.03→34.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2303 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.861 / SU B: 6.273 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1279 / SU Rfree: 0.1296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 1678 5.1 %RANDOM
Rwork0.1901 ---
all0.192 33474 --
obs0.192 33153 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 183.28 Å2 / Biso mean: 40.9279 Å2 / Biso min: 15.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--1.3 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.03→34.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 8 219 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022165
X-RAY DIFFRACTIONr_bond_other_d0.0010.021460
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9722952
X-RAY DIFFRACTIONr_angle_other_deg0.98833600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3825270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.08625.278108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83315394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1191511
X-RAY DIFFRACTIONr_chiral_restr0.0960.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 117 -
Rwork0.305 2010 -
all-2127 -
obs--92.8 %
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)
10.022-0.1475-0.08712.70250.98871.04220.0361-0.01630.0083-0.2049-0.15260.20690.04030.10.11650.23980.00420.01980.0684-0.03340.059221.196113.6958-0.7635
21.32340.1813-0.60080.40530.27660.7296-0.0214-0.0813-0.0550.031-0.0077-0.01660.06430.04580.02920.0770.0161-0.00080.09690.00980.071343.141545.8138.6681
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1398 - 1516
2X-RAY DIFFRACTION2A1517 - 1652

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