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- PDB-4yc9: Crystal structure of TRIM24 PHD-bromodomain complexed with N-(6-{... -

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Basic information

Entry
Database: PDB / ID: 4yc9
TitleCrystal structure of TRIM24 PHD-bromodomain complexed with N-(6-{3-[4-(dimethylamino)butoxy]-5-propoxyphenoxy}-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl)-3,4-dimethoxybenzene-1-sulfonamide (8i)
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 / regulation of signal transduction by p53 class mediator / epithelial cell proliferation ...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 / regulation of signal transduction by p53 class mediator / epithelial cell proliferation / nuclear receptor binding / male germ cell nucleus / protein catabolic process / euchromatin / response to peptide hormone / RING-type E3 ubiquitin transferase / regulation of protein stability / negative regulation of epithelial cell proliferation / p53 binding / ubiquitin protein ligase activity / Signaling by BRAF and RAF1 fusions / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4C1 / Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,1845
Polymers21,3181
Non-polymers8664
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.839, 35.624, 65.367
Angle α, β, γ (deg.)90.000, 112.070, 90.000
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-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-4C1 / N-(6-{3-[4-(dimethylamino)butoxy]-5-propoxyphenoxy}-1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)-3,4-dimethoxybenzenesulfonamide


Mass: 642.763 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H42N4O8S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 45.9 %
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: Feb 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.82→60.576 Å / Num. all: 17452 / Num. obs: 17452 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rpim(I) all: 0.056 / Rrim(I) all: 0.111 / Rsym value: 0.088 / Net I/av σ(I): 5.565 / Net I/σ(I): 7 / Num. measured all: 66226
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.82-1.923.80.5151.4952825150.3280.515299.5
1.92-2.033.90.3222.2926323950.2030.322399.8
2.03-2.183.90.2133.3872322570.1320.2134.499.9
2.18-2.353.90.1753.9803620850.1110.1755.799.8
2.35-2.573.80.1235.4739719340.0770.1237.299.9
2.57-2.883.80.1056671517610.0650.1058.9100
2.88-3.323.80.0896.9589615630.0530.08911.199.8
3.32-4.073.70.0728.7481113170.0440.07214.199.8
4.07-5.763.50.05111.6360110270.0350.05114.399.4
5.76-60.5763.80.04911.922565980.0350.04914.499.8

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O34

3o34


Resolution: 1.82→42.58 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.286 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 847 4.9 %RANDOM
Rwork0.155 ---
obs0.1575 16574 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.41 Å2 / Biso mean: 36.339 Å2 / Biso min: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.82→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 53 214 1715
Biso mean--46.2 49.4 -
Num. residues----180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021538
X-RAY DIFFRACTIONr_bond_other_d0.0040.021428
X-RAY DIFFRACTIONr_angle_refined_deg1.8692.0252086
X-RAY DIFFRACTIONr_angle_other_deg1.1143.0093316
X-RAY DIFFRACTIONr_chiral_restr0.1070.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02327
X-RAY DIFFRACTIONr_mcbond_it3.5313.223718
X-RAY DIFFRACTIONr_mcbond_other3.5023.219717
X-RAY DIFFRACTIONr_mcangle_it4.924.8894
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 63 -
Rwork0.274 1219 -
all-1282 -
obs--98.77 %

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