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

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Basic information

Entry
Database: PDB / ID: 4ybm
TitleCrystal structure of TRIM24 PHD-bromodomain complexed with N-{6-[3-(benzyloxy)phenoxy]-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-3,4-dimethoxybenzene-1-sulfonamide (7b)
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-4BJ / Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 18, 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)44,61014
Polymers42,6372
Non-polymers1,97312
Water10,377576
1
A: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6335
Polymers21,3181
Non-polymers3154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9779
Polymers21,3181
Non-polymers1,6588
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.400, 79.820, 131.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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)

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Non-polymers , 5 types, 588 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-4BJ / N-{6-[3-(benzyloxy)phenoxy]-1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}-3,4-dimethoxybenzenesulfonamide


Mass: 575.632 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H29N3O7S
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
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: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.46→34.13 Å / Num. obs: 68336 / % possible obs: 99.2 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.9
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.155 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Aimless0.1.27data scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O34

3o34


Resolution: 1.46→33.87 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.337 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.196 3461 5.1 %RANDOM
Rwork0.163 ---
obs0.165 64733 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.77 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.46→33.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 120 576 3517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.023061
X-RAY DIFFRACTIONr_bond_other_d0.0020.022801
X-RAY DIFFRACTIONr_angle_refined_deg2.1892.0284162
X-RAY DIFFRACTIONr_angle_other_deg0.9963.0066511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9415355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94925.352142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84415519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1831510
X-RAY DIFFRACTIONr_chiral_restr0.1320.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213394
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02664
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: 1.46→1.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 232 -
Rwork0.352 4812 -
obs--99.98 %

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