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- PDB-4zql: Crystal structure of TRIM24 with 3,4-dimethoxy-N-(6-(4-methoxyphe... -

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Basic information

Entry
Database: PDB / ID: 4zql
TitleCrystal structure of TRIM24 with 3,4-dimethoxy-N-(6-(4-methoxyphenoxy)-1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)benzenesulfonamide inhibitor
ComponentsTranscription intermediary factor 1-alpha
KeywordsLIGASE / Transcriptional coactivator / histone H3 modifications / E3 protein-ubiquitin ligase activity / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H3K23ac reader activity / 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 / nuclear receptor binding ...histone H3K23ac reader activity / 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 / nuclear receptor binding / regulation of signal transduction by p53 class mediator / male germ cell nucleus / protein catabolic process / regulation of protein stability / euchromatin / 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 / protein kinase activity / transcription coactivator 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-4QH / Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsTallant, C. / Structural Genomics Consortium (SGC) / Clark, P.G.K. / Vieira, L.C.C. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Fedorov, O. / Dixon, D.J. / von Delft, F. ...Tallant, C. / Structural Genomics Consortium (SGC) / Clark, P.G.K. / Vieira, L.C.C. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Fedorov, O. / Dixon, D.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Knapp, S.
CitationJournal: To Be Published
Title: Crystal structure of TRIM24 with 3,4-dimethoxy-N-(6-(4-methoxyphenoxy)-1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)benzenesulfonamide inhibitor
Authors: Clark, P.G. / Vieira, L.C. / Tallant, C. / Fedorov, O. / Singleton, D.C. / Rogers, C.M. / Monteiro, O.P. / Bennett, J.M. / Baronio, R. / Muller, S. / Daniels, D.L. / Mendez, J. / Knapp, S. / ...Authors: Clark, P.G. / Vieira, L.C. / Tallant, C. / Fedorov, O. / Singleton, D.C. / Rogers, C.M. / Monteiro, O.P. / Bennett, J.M. / Baronio, R. / Muller, S. / Daniels, D.L. / Mendez, J. / Knapp, S. / Brennan, P.E. / Dixon, D.J.
History
DepositionMay 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 intermediary factor 1-alpha
B: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,07711
Polymers42,8072
Non-polymers1,2709
Water3,747208
1
A: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7095
Polymers21,4041
Non-polymers3054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3686
Polymers21,4041
Non-polymers9655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.414, 36.661, 128.989
Angle α, β, γ (deg.)90.00, 109.87, 90.00
Int Tables number5
Space group name H-MC121

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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: 21403.547 Da / Num. of mol.: 2 / Fragment: residues 791-972
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM24, RNF82, TIF1, TIF1A / Plasmid: pET15 / Production host: Escherichia coli (E. coli)
References: UniProt: O15164, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 6 types, 217 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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: Chemical ChemComp-4QH / 3,4-dimethoxy-N-[6-(4-methoxyphenoxy)-1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl]benzenesulfonamide


Mass: 499.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25N3O7S
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density meas: 397644.281 Mg/m3 / Density % sol: 48.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 2M ammonium sulfate, 2%(v/v) PEG 400
PH range: 7.5-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.79→27.84 Å / Num. all: 37097 / Num. obs: 37097 / % possible obs: 99.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.055 / Rsym value: 0.027 / Net I/σ(I): 17.3
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 3.2 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O33

3o33


Resolution: 1.79→27.84 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.115 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19904 1856 5 %RANDOM
Rwork0.15883 ---
obs0.16083 35229 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.473 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å2-1.39 Å2
2---0.01 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.79→27.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 69 208 3145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023002
X-RAY DIFFRACTIONr_bond_other_d0.0010.022789
X-RAY DIFFRACTIONr_angle_refined_deg1.6582.0094061
X-RAY DIFFRACTIONr_angle_other_deg0.863.0036482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6375349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27525.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80815527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8551510
X-RAY DIFFRACTIONr_chiral_restr0.1080.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213291
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02639
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_it3.2594.0121408
X-RAY DIFFRACTIONr_mcbond_other3.2524.011407
X-RAY DIFFRACTIONr_mcangle_it4.1287.4431753
X-RAY DIFFRACTIONr_mcangle_other4.1317.4441754
X-RAY DIFFRACTIONr_scbond_it6.1755.2711594
X-RAY DIFFRACTIONr_scbond_other6.1735.2741595
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1819.2872309
X-RAY DIFFRACTIONr_long_range_B_refined9.67825.1793520
X-RAY DIFFRACTIONr_long_range_B_other9.57524.7923442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.793→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 134 -
Rwork0.227 2356 -
obs--91.01 %
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)Details (eV)Origin x (Å)Origin y (Å)Origin z (Å)
10.94240.06550.19061.4842-0.39121.92420.0242-0.08170.0516-0.1599-0.01240.04910.0474-0.0438-0.01180.05380.0023-0.02570.008-0.00680.018Chain A21.2622.3315.148
21.24880.46280.39570.94020.29051.10080.01310.0763-0.01770.03050.027-0.0271-0.01390.0039-0.040.017-0.0037-0.02270.00780.00710.0349Chain B-4.0232.93346.088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B825 - 1006
2X-RAY DIFFRACTION2B825 - 1006

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