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- PDB-3hmh: Crystal structure of the second bromodomain of human TBP-associat... -

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Basic information

Entry
Database: PDB / ID: 3hmh
TitleCrystal structure of the second bromodomain of human TBP-associated factor RNA polymerase 1-like (TAF1L)
ComponentsTranscription initiation factor TFIID 210 kDa subunit
KeywordsTRANSCRIPTION / MGC134910 / TAF2A2 / Structural Genomics Consortium / SGC / Bromodomain / Cell cycle / Disulfide bond / DNA-binding / Nucleus / Transcription regulation
Function / homology
Function and homology information


male meiotic nuclear division / RNA polymerase II general transcription initiation factor binding / 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 ...male meiotic nuclear division / RNA polymerase II general transcription initiation factor binding / 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 / lysine-acetylated histone 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 1-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Keates, T. / Zhang, Y. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. ...Filippakopoulos, P. / Picaud, S. / Keates, T. / Zhang, Y. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / 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
DepositionMay 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor TFIID 210 kDa subunit


Theoretical massNumber of molelcules
Total (without water)18,0231
Polymers18,0231
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcription initiation factor TFIID 210 kDa subunit

A: Transcription initiation factor TFIID 210 kDa subunit


Theoretical massNumber of molelcules
Total (without water)36,0472
Polymers36,0472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2320 Å2
ΔGint-14 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.139, 55.139, 84.441
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-22-

HOH

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Components

#1: Protein Transcription initiation factor TFIID 210 kDa subunit / TAF1L / TBP-associated factor 210 kDa / TAF(II)210 / TBP-associated factor 1-like


Mass: 18023.252 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 1523-1651
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1L / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q8IZX4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.06 Å3/Da / Density % sol: 40.17 % / Mosaicity: 0.78 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15w/v PEG_3350, 0.17M ammonium_sulfate, 15w/v glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.05→28.15 Å / Num. all: 9764 / Num. obs: 9764 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 15.6
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1392 / Rsym value: 0.687 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.99 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.15 Å
Translation2.5 Å28.15 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

2nxb

2oo1

2oss

2ouo

2rfj

3dai

3d7c

3dwy


Resolution: 2.05→28.15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.169 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.838 / SU B: 11.214 / SU ML: 0.135 / SU R Cruickshank DPI: 0.199 / SU Rfree: 0.191 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.252 496 5.1 %RANDOM
Rwork0.181 ---
all0.185 9741 --
obs0.185 9738 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.38 Å2 / Biso mean: 18.147 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 0 0 68 1200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221167
X-RAY DIFFRACTIONr_bond_other_d0.0010.02764
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9491585
X-RAY DIFFRACTIONr_angle_other_deg0.94831888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8325138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.20126.16760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47815209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.848152
X-RAY DIFFRACTIONr_chiral_restr0.0910.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02215
X-RAY DIFFRACTIONr_mcbond_it3.7663701
X-RAY DIFFRACTIONr_mcbond_other1.2673273
X-RAY DIFFRACTIONr_mcangle_it5.22551151
X-RAY DIFFRACTIONr_scbond_it9.1368466
X-RAY DIFFRACTIONr_scangle_it11.33511434
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 42 -
Rwork0.281 661 -
all-703 -
obs--100 %
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)
11.9327-1.7692.56631.7728-2.10685.68030.1184-0.0234-0.1317-0.12160.04020.17730.0634-0.1309-0.15860.1138-0.0308-0.00910.0655-0.02520.141639.337814.797613.6242
21.109-0.41970.4422.1017-1.41013.50120.10920.1934-0.0278-0.1641-0.1534-0.06370.28880.37520.04420.18350.0255-0.02020.0963-0.06850.159644.3738.214511.0857
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1513 - 1588
2X-RAY DIFFRACTION2A1589 - 1651

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