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- PDB-4ybs: Crystal structure of TRIM24 PHD-bromodomain complexed with N-{1,3... -

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Basic information

Entry
Database: PDB / ID: 4ybs
TitleCrystal structure of TRIM24 PHD-bromodomain complexed with N-{1,3-dimethyl-6-[3-(2-methylpropoxy)phenoxy]-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-1,2-dimethyl-1H-imidazole-4-sulfonamide (7g)
ComponentsTranscription intermediary factor 1-alpha
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / Center for Biomolecular Structure and Function / Bromodomain / TRIM24 / inhibitor / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
Function / homology
Function and homology information


perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / cellular response to estrogen stimulus / estrogen response element binding / calcium ion homeostasis / Signaling by FGFR1 in disease / epithelial cell proliferation / regulation of signal transduction by p53 class mediator / male germ cell nucleus ...perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / cellular response to estrogen stimulus / estrogen response element binding / calcium ion homeostasis / Signaling by FGFR1 in disease / epithelial cell proliferation / regulation of signal transduction by p53 class mediator / male germ cell nucleus / nuclear receptor binding / lysine-acetylated histone binding / RING-type E3 ubiquitin transferase / regulation of protein stability / euchromatin / protein catabolic process / response to peptide hormone / negative regulation of epithelial cell proliferation / Signaling by BRAF and RAF1 fusions / ubiquitin protein ligase activity / p53 binding / regulation of apoptotic process / transcription by RNA polymerase II / transcription coactivator activity / protein kinase activity / protein ubiquitination / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / chromatin / mitochondrion / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. ...B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, PHD-type, conserved site / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4BK / Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsPoncet-Montange, G. / Palmer, W. / Jones, P.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Structure-Guided Design of IACS-9571, a Selective High-Affinity Dual TRIM24-BRPF1 Bromodomain Inhibitor.
Authors: Palmer, W.S. / Poncet-Montange, G. / Liu, G. / Petrocchi, A. / Reyna, N. / Subramanian, G. / Theroff, J. / Yau, A. / Kost-Alimova, M. / Bardenhagen, J.P. / Leo, E. / Shepard, H.E. / Tieu, T. ...Authors: Palmer, W.S. / Poncet-Montange, G. / Liu, G. / Petrocchi, A. / Reyna, N. / Subramanian, G. / Theroff, J. / Yau, A. / Kost-Alimova, M. / Bardenhagen, J.P. / Leo, E. / Shepard, H.E. / Tieu, T.N. / Shi, X. / Zhan, Y. / Zhao, S. / Barton, M.C. / Draetta, G. / Toniatti, C. / Jones, P. / Geck Do, M. / Andersen, J.N.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0275
Polymers21,3181
Non-polymers7094
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.735, 36.238, 65.935
Angle α, β, γ (deg.)90.00, 111.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcription intermediary factor 1-alpha / TIF1-alpha / E3 ubiquitin-protein ligase TRIM24 / RING finger protein 82 / Tripartite motif- ...TIF1-alpha / E3 ubiquitin-protein ligase TRIM24 / RING finger protein 82 / Tripartite motif-containing protein 24


Mass: 21318.395 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 824-1006)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM24, RNF82, TIF1, TIF1A / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O15164, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-4BK / N-{1,3-dimethyl-6-[3-(2-methylpropoxy)phenoxy]-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}-1,2-dimethyl-1H-imidazole-4-sulfonamide


Mass: 499.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29N5O5S
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.2-2.4M ammonium sulfate, 0.1M HEPES buffer pH 7.5, 2% PEG400 and 8-9% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.83→61.322 Å / Num. obs: 17778 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rsym value: 0.055 / Net I/σ(I): 10
Reflection shellResolution: 1.83→1.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.339 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O34

3o34


Resolution: 1.83→61.32 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.911 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.231 909 5.1 %RANDOM
Rwork0.167 ---
obs0.17 16828 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.83→61.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 41 146 1633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021524
X-RAY DIFFRACTIONr_bond_other_d0.0010.021419
X-RAY DIFFRACTIONr_angle_refined_deg1.9472.0212068
X-RAY DIFFRACTIONr_angle_other_deg0.9513.0063296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2085176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24225.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13115264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.736155
X-RAY DIFFRACTIONr_chiral_restr0.1190.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 60 -
Rwork0.31 1258 -
obs--98.95 %

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