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- PDB-6df7: TAF1-BD2 in complex with Cpd27 (6-(but-3-en-1-yl)-4-(1-methyl-6-(... -

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Basic information

Entry
Database: PDB / ID: 6df7
TitleTAF1-BD2 in complex with Cpd27 (6-(but-3-en-1-yl)-4-(1-methyl-6-(morpholine-4-carbonyl)-1H-benzo[d]imidazol-4-yl)-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one)
ComponentsTranscription initiation factor TFIID subunit
KeywordsTranscription/Inhibitor / TAF1-BD2 / Bromodomain / small molecule inhibitor / SBDD / Transcription-Inhibitor complex
Function / homology
Function and homology information


RNA polymerase II general transcription initiation factor binding / transcription factor TFIID complex / histone acetyltransferase activity / TBP-class protein binding / DNA-templated transcription initiation / transcription by RNA polymerase II / cell cycle / protein serine/threonine kinase activity / DNA binding / membrane
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
Chem-G9V / Transcription initiation factor TFIID subunit
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMurray, J.M.
CitationJournal: J. Med. Chem. / Year: 2018
Title: GNE-371, a Potent and Selective Chemical Probe for the Second Bromodomains of Human Transcription-Initiation-Factor TFIID Subunit 1 and Transcription-Initiation-Factor TFIID Subunit 1-like.
Authors: Wang, S. / Tsui, V. / Crawford, T.D. / Audia, J.E. / Burdick, D.J. / Beresini, M.H. / Cote, A. / Cummings, R. / Duplessis, M. / Flynn, E.M. / Hewitt, M.C. / Huang, H.R. / Jayaram, H. / ...Authors: Wang, S. / Tsui, V. / Crawford, T.D. / Audia, J.E. / Burdick, D.J. / Beresini, M.H. / Cote, A. / Cummings, R. / Duplessis, M. / Flynn, E.M. / Hewitt, M.C. / Huang, H.R. / Jayaram, H. / Jiang, Y. / Joshi, S. / Murray, J. / Nasveschuk, C.G. / Pardo, E. / Poy, F. / Romero, F.A. / Tang, Y. / Taylor, A.M. / Wang, J. / Xu, Z. / Zawadzke, L.E. / Zhu, X. / Albrecht, B.K. / Magnuson, S.R. / Bellon, S. / Cochran, A.G.
History
DepositionMay 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: Transcription initiation factor TFIID subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4684
Polymers38,6052
Non-polymers8632
Water3,351186
1
A: Transcription initiation factor TFIID subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7342
Polymers19,3031
Non-polymers4311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription initiation factor TFIID subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7342
Polymers19,3031
Non-polymers4311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.415, 79.701, 83.828
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


Mass: 19302.543 Da / Num. of mol.: 2 / Fragment: Bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: TAF1 / Production host: Escherichia coli (E. coli) / References: UniProt: U3KMH2
#2: Chemical ChemComp-G9V / 6-(but-3-en-1-yl)-4-[1-methyl-6-(morpholine-4-carbonyl)-1H-benzimidazol-4-yl]-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one


Mass: 431.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N5O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1 M BIS-TRIS pH 6.5, 28% w/v PEG MME 2,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→41.914 Å / Num. obs: 22773 / % possible obs: 93.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 45.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.035 / Rrim(I) all: 0.093 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.003-2.017.52.2432190.3640.872.407100
9.264-41.9145.10.0382620.9980.0170.04289.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i1q

5i1q


Resolution: 2→21.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.176 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.149
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1131 4.97 %RANDOM
Rwork0.195 ---
obs0.197 22754 93.8 %-
Displacement parametersBiso max: 154.06 Å2 / Biso mean: 50.37 Å2 / Biso min: 27.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.9237 Å20 Å20 Å2
2---1.2048 Å20 Å2
3---2.1285 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2→21.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 64 186 2339
Biso mean--39.06 61.04 -
Num. residues----256
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d757SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes380HARMONIC5
X-RAY DIFFRACTIONt_it2214HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion287SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2693SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2214HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3017HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion19.09
LS refinement shellResolution: 2→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2342 116 4.48 %
Rwork0.2313 2471 -
all0.2314 2587 -
obs--81.23 %
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)
10.6098-0.16350.156300.14121.2777-0.0483-0.21430.07210.03530.1054-0.0942-0.2070.0086-0.0571-0.0006-0.0069-0.0326-0.0621-0.01680.013623.1005-0.045686.0482
21.126-0.2767-0.41482.41731.57153.2711-0.1472-0.13120.02390.19970.2669-0.06960.03760.3873-0.1197-0.08050.07590.0206-0.04050.0174-0.040320.8424-19.10999.6855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1501 - 1635
2X-RAY DIFFRACTION2{ B|* }B1501 - 1621

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