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- PDB-9gdg: Crystal structure of TRIM24 PHD-BRD in complex with N-(2-(2-(2-ac... -

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Basic information

Entry
Database: PDB / ID: 9gdg
TitleCrystal structure of TRIM24 PHD-BRD in complex with N-(2-(2-(2-acetamidoethoxy)ethoxy)ethyl)-3-(N-(1,3-dimethyl-2-oxo-6-(3-propoxyphenoxy)-2,3-dihydro-1H-benzo[d]imidazol-5-yl)sulfamoyl)benzamide (PEG linker unresolved)
ComponentsTranscription intermediary factor 1-alpha
KeywordsTRANSCRIPTION / Transcriptional regulation / PHD / Bromodomain
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 / 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 ubiquitination / protein kinase activity / 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 finger, PHD-type, conserved site / PHD-finger / 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 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 / 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
Similarity search - Domain/homology
: / Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.462 Å
AuthorsPlatt, M.A. / Kot, E. / Conway, S.J. / Koekemoer, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008784/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of TRIM24 PHD-BRD in complex with N-(2-(2-(2-acetamidoethoxy)ethoxy)ethyl)-3-(N-(1,3-dimethyl-2-oxo-6-(3-propoxyphenoxy)-2,3-dihydro-1H-benzo[d]imidazol-5-yl)sulfamoyl) ...Title: Crystal structure of TRIM24 PHD-BRD in complex with N-(2-(2-(2-acetamidoethoxy)ethoxy)ethyl)-3-(N-(1,3-dimethyl-2-oxo-6-(3-propoxyphenoxy)-2,3-dihydro-1H-benzo[d]imidazol-5-yl)sulfamoyl)benzamide (PEG linker unresolved)
Authors: Platt, M.A. / Kot, E. / Conway, S.J. / Koekemoer, L.
History
DepositionAug 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,2964
Polymers21,4821
Non-polymers8153
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10810 Å2
Unit cell
Length a, b, c (Å)90.942, 36.652, 65.456
Angle α, β, γ (deg.)90, 111.325, 90
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 / RING-type E3 ubiquitin ...TIF1-alpha / E3 ubiquitin-protein ligase TRIM24 / RING finger protein 82 / RING-type E3 ubiquitin transferase TIF1-alpha / Tripartite motif-containing protein 24


Mass: 21481.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM24, RNF82, TIF1, TIF1A / Production host: Escherichia coli (E. coli)
References: UniProt: O15164, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-A1IKF / N-(2-(2-(2-acetamidoethoxy)ethoxy)ethyl)-3-(N-(1,3-dimethyl-2-oxo-6-(3-propoxyphenoxy)-2,3-dihydro-1H-benzo[d]imidazol-5-yl)sulfamoyl)benzamide


Mass: 683.772 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H41N5O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 1.8 M ammonium sulfate, 0.1 M HEPES (pH 7.3), 5% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.46→60.974 Å / Num. obs: 23849 / % possible obs: 84.9 % / Redundancy: 6.44 % / Rrim(I) all: 0.051 / Net I/σ(I): 18.5
Reflection shellResolution: 1.46→1.64 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1192 / Rrim(I) all: 0.623

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.77)refinement
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.462→60.974 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.446 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.094
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2098 1232 5.166 %
Rwork0.1499 22616 -
all0.153 --
obs-23848 67.98 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.956 Å2
Baniso -1Baniso -2Baniso -3
1-0.043 Å2-0 Å20.032 Å2
2---0.159 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.462→60.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 0 50 119 1600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121517
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161393
X-RAY DIFFRACTIONr_angle_refined_deg2.1751.8522054
X-RAY DIFFRACTIONr_angle_other_deg0.7791.7653242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.5347.91712
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37410263
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.7661070
X-RAY DIFFRACTIONr_chiral_restr0.1370.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021711
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02325
X-RAY DIFFRACTIONr_nbd_refined0.2220.2288
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.21229
X-RAY DIFFRACTIONr_nbtor_refined0.1960.2732
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2813
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.291
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.210
X-RAY DIFFRACTIONr_nbd_other0.3140.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.216
X-RAY DIFFRACTIONr_mcbond_it8.2422.252702
X-RAY DIFFRACTIONr_mcbond_other8.1982.251702
X-RAY DIFFRACTIONr_mcangle_it11.4524.038874
X-RAY DIFFRACTIONr_mcangle_other11.4544.038875
X-RAY DIFFRACTIONr_scbond_it12.5172.803815
X-RAY DIFFRACTIONr_scbond_other12.5122.803816
X-RAY DIFFRACTIONr_scangle_it17.4784.9221180
X-RAY DIFFRACTIONr_scangle_other17.4714.9341181
X-RAY DIFFRACTIONr_lrange_it18.87626.5311756
X-RAY DIFFRACTIONr_lrange_other18.80425.6251726
X-RAY DIFFRACTIONr_rigid_bond_restr7.38632910
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc work% reflection obs (%)WRfactor RworkFsc free
1.462-1.50.00510.241510.23525460.9592.04240.238
1.5-1.5410.140.1941540.19125260.976.25490.1880.991
1.541-1.5860.296190.2013210.20624410.9713.92870.1940.929
1.586-1.6340.223390.1995450.20123620.96924.72480.1850.959
1.634-1.6880.225580.1999680.222940.97144.72540.1820.964
1.688-1.7470.244740.17213850.17622520.97864.78690.1560.961
1.747-1.8130.239770.15916890.16321400.98382.52340.1410.964
1.813-1.8870.1811110.13819280.14120720.98798.40730.1180.978
1.887-1.9710.226920.1318880.13519800.9851000.1140.956
1.971-2.0670.21970.12117780.12518760.99199.94670.1090.969
2.067-2.1780.2211010.11517260.1218270.9921000.1050.967
2.178-2.310.198890.11716200.12117120.99299.82480.1090.977
2.31-2.470.19750.1315440.13316220.98999.8150.1250.976
2.47-2.6670.223680.14114380.14415070.98899.93360.1420.976
2.667-2.9210.222750.15713150.16113900.9841000.1640.97
2.921-3.2650.21790.17811970.1812770.9899.92170.1910.97
3.265-3.7680.197510.15510630.15711170.98799.73140.1750.981
3.768-4.6110.186500.1378890.149390.9881000.1710.976
4.611-6.5020.226480.1867050.1887550.98199.73510.2290.968
6.502-60.9740.219240.1934110.1944360.97799.77060.2750.97

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