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- PDB-3uv4: Crystal Structure of the second bromodomain of human Transcriptio... -

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Basic information

Entry
Database: PDB / ID: 3uv4
TitleCrystal Structure of the second bromodomain of human Transcription initiation factor TFIID subunit 1 (TAF1)
Componentssecond bromodomain of human Transcription initiation factor TFIID subunit 1 (TAF1)
KeywordsTRANSCRIPTION / 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
PHOSPHATE ION / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Keates, T. / Ugochukwu, E. / 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 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: second bromodomain of human Transcription initiation factor TFIID subunit 1 (TAF1)
B: second bromodomain of human Transcription initiation factor TFIID subunit 1 (TAF1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0827
Polymers36,7092
Non-polymers3735
Water5,495305
1
A: second bromodomain of human Transcription initiation factor TFIID subunit 1 (TAF1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5093
Polymers18,3541
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: second bromodomain of human Transcription initiation factor TFIID subunit 1 (TAF1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5744
Polymers18,3541
Non-polymers2193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.450, 57.800, 123.570
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 second bromodomain of human Transcription initiation factor TFIID subunit 1 (TAF1) / 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: 18354.488 Da / Num. of mol.: 2 / Fragment: unp residues 1501-1635
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density meas: 55.98 Mg/m3 / Density % sol: 55.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.056M NaH2PO4 1.344M K2HPO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.52 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52 Å / Relative weight: 1
ReflectionRedundancy: 4.7 % / Av σ(I) over netI: 9.7 / Number: 158114 / Rsym value: 0.074 / D res high: 1.89 Å / D res low: 28.9 Å / Num. obs: 33417 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.9828.999.110.020.024.3
4.235.9810010.0240.0244.7
3.454.2310010.0330.0334.7
2.993.4510010.0530.0534.8
2.672.9999.810.0810.0814.8
2.442.6799.710.1380.1384.8
2.262.4499.410.2020.2024.8
2.112.2698.910.2840.2844.8
1.992.1198.610.4730.4734.7
1.891.9997.810.7630.7634.7
ReflectionResolution: 1.89→28.96 Å / Num. all: 33686 / Num. obs: 33417 / % possible obs: 99.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.89-1.994.70.76312238747340.76397.8
1.99-2.114.70.4731.62129244920.47398.6
2.11-2.264.80.2842.72031042690.28498.9
2.26-2.444.80.2023.81905040060.20299.4
2.44-2.674.80.1385.61766337080.13899.7
2.67-2.994.80.0819.41615633780.08199.8
2.99-3.454.80.05313.61439930250.053100
3.45-4.234.70.03321.71218225750.033100
4.23-5.984.70.02427.5948320330.024100
5.98-28.94.30.0229.2519211970.0299.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 57.15 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.9 Å
Translation2.5 Å28.9 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata 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: 1.89→28.96 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.1994 / WRfactor Rwork: 0.1691 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8694 / SU B: 6.168 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1199 / SU Rfree: 0.1188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rwork0.1906 ---
all0.1924 33666 --
obs0.1924 33238 98.73 %-
Rfree---RANDOM
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.86 Å2 / Biso mean: 28.982 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.89→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 23 305 2336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222084
X-RAY DIFFRACTIONr_bond_other_d0.0010.021340
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9462835
X-RAY DIFFRACTIONr_angle_other_deg0.95533305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8895249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.66225.922103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50515344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.594154
X-RAY DIFFRACTIONr_chiral_restr0.090.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212285
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02385
X-RAY DIFFRACTIONr_mcbond_it3.15731267
X-RAY DIFFRACTIONr_mcbond_other1.093490
X-RAY DIFFRACTIONr_mcangle_it4.41352081
X-RAY DIFFRACTIONr_scbond_it6.8038817
X-RAY DIFFRACTIONr_scangle_it8.36311754
LS refinement shellResolution: 1.891→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 123 -
Rwork0.322 2193 -
all-2316 -
obs--94.26 %
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)
12.0253-1.12050.536710.615-2.1582.21380.16090.0027-0.1694-0.2426-0.12720.04350.24050.0533-0.03370.0934-0.02250.01380.0634-0.03010.0329-0.129-4.038335.1292
22.3397-0.864-0.27364.92220.95542.4610.0711-0.0397-0.04750.0587-0.007-0.26540.10690.2319-0.06410.0761-0.02240.01260.0928-0.0350.03714.63533.048839.6947
34.63570.2443-0.06181.4083-0.0871.9289-0.1369-0.06070.2097-0.02050.0878-0.0012-0.128-0.06390.04910.069-0.00880.00820.0707-0.06040.0608-8.673417.723255.1922
410.84270.36572.8882.09140.04152.6142-0.02280.0392-0.4189-0.12060.02980.15390.0804-0.2585-0.00710.1016-0.0390.03810.104-0.04660.0625-13.56098.671649.2886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1520 - 1550
2X-RAY DIFFRACTION2A1551 - 1644
3X-RAY DIFFRACTION3B1520 - 1606
4X-RAY DIFFRACTION4B1607 - 1645

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