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- PDB-4yab: Crystal structure of TRIM24 PHD-bromodomain complexed with 1-meth... -

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Basic information

Entry
Database: PDB / ID: 4yab
TitleCrystal structure of TRIM24 PHD-bromodomain complexed with 1-methyl-5-(2-methyl-1 3-thiazol-4-yl)-2 3-dihydro-1H-indol-2-one (1)
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 / male germ cell nucleus / epithelial cell proliferation / regulation of signal transduction by p53 class mediator ...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 / male germ cell nucleus / epithelial cell proliferation / regulation of signal transduction by p53 class mediator / nuclear receptor binding / : / protein catabolic process / euchromatin / regulation of protein stability / RING-type E3 ubiquitin transferase / response to peptide hormone / negative regulation of epithelial cell proliferation / p53 binding / Signaling by BRAF and RAF1 fusions / ubiquitin protein ligase activity / 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, PHD-type, conserved site / PHD-finger ...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, PHD-type, conserved site / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-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-4CN / Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 17, 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
B: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,57910
Polymers42,6372
Non-polymers9428
Water7,278404
1
A: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7905
Polymers21,3181
Non-polymers4714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7905
Polymers21,3181
Non-polymers4714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.640, 36.950, 128.921
Angle α, β, γ (deg.)90.00, 110.03, 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.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-4CN / 1-methyl-5-(2-methyl-1,3-thiazol-4-yl)-1,3-dihydro-2H-indol-2-one


Mass: 244.312 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N2OS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
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: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.9→60.56 Å / Num. obs: 29120 / % possible obs: 92.7 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.037 / Net I/σ(I): 12.8 / Num. measured all: 180291 / Scaling rejects: 70
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.9-1.946.40.7472.21152118050.8020.31788.8
9.11-60.566.60.03132.221543270.9990.01399.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimless0.3.11data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O34

3o34


Resolution: 1.9→60.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.762 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1430 4.9 %RANDOM
Rwork0.161 ---
obs0.164 27687 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→60.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 0 48 404 3313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023030
X-RAY DIFFRACTIONr_bond_other_d0.0010.022814
X-RAY DIFFRACTIONr_angle_refined_deg1.7942.0054117
X-RAY DIFFRACTIONr_angle_other_deg0.9013.0026553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91225.319141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21815537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0051510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213357
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02649
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_it3.0043.11427
X-RAY DIFFRACTIONr_mcbond_other3.0033.0991426
X-RAY DIFFRACTIONr_mcangle_it4.3894.6141784
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 84 -
Rwork0.27 1955 -
obs--88.42 %

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