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- PDB-5h1t: Complex structure of TRIM24 PHD-bromodomain and inhibitor 1 -

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Basic information

Entry
Database: PDB / ID: 5h1t
TitleComplex structure of TRIM24 PHD-bromodomain and inhibitor 1
ComponentsTranscription intermediary factor 1-alpha
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / TRANSCRIPTION / TRANSCRIPTION 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 / calcium ion homeostasis / cellular response to estrogen stimulus / estrogen response element binding / Signaling by FGFR1 in disease / regulation of signal transduction by p53 class mediator / epithelial cell proliferation / male germ cell nucleus ...perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / calcium ion homeostasis / cellular response to estrogen stimulus / estrogen response element binding / Signaling by FGFR1 in disease / regulation of signal transduction by p53 class mediator / epithelial cell proliferation / male germ cell nucleus / nuclear receptor binding / euchromatin / protein catabolic process / lysine-acetylated histone binding / RING-type E3 ubiquitin transferase / regulation of protein stability / response to peptide hormone / negative regulation of epithelial cell proliferation / ubiquitin protein ligase activity / Signaling by BRAF and RAF1 fusions / p53 binding / 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 / 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, 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, PHD-type, conserved site / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-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-7FF / Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsLiu, J.
CitationJournal: FEBS J. / Year: 2017
Title: The polar warhead of a TRIM24 bromodomain inhibitor rearranges a water-mediated interaction network
Authors: Liu, J. / Li, F. / Bao, H. / Jiang, Y. / Zhang, S. / Ma, R. / Gao, J. / Wu, J. / Ruan, K.
History
DepositionOct 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 8, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,43018
Polymers84,9254
Non-polymers1,50514
Water4,360242
1
A: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6475
Polymers21,2311
Non-polymers4154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10320 Å2
MethodPISA
2
B: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6475
Polymers21,2311
Non-polymers4154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20 Å2
ΔGint-4 kcal/mol
Surface area10970 Å2
MethodPISA
3
C: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5684
Polymers21,2311
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10690 Å2
MethodPISA
4
D: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5684
Polymers21,2311
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.725, 48.612, 123.454
Angle α, β, γ (deg.)86.560, 81.470, 67.810
Int Tables number1
Space group name H-MP1

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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: 21231.316 Da / Num. of mol.: 4 / Fragment: UNP residues 824-1006
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM24, RNF82, TIF1, TIF1A
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): 'BL21-Gold(DE3)pLysS AG'
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.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-7FF / methyl 6-azanyl-3,4-dihydro-2H-quinoline-1-carboxylate


Mass: 206.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14N2O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium, 2%(v/v) Polyethylene glycol 400, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 52566 / % possible obs: 92.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.98 Å2 / Rmerge(I) obs: 0.089 / Net I/av σ(I): 15.147 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.95-2.023.40.5420.843191
2.02-2.13.50.3920.883189.1
2.1-2.23.70.3160.934194.1
2.2-2.313.70.2640.921193.4
2.31-2.463.60.1680.977191.7
2.46-2.653.70.1270.984192.4
2.65-2.913.70.1050.986194.3
2.91-3.333.70.0750.993190.6
3.33-4.23.80.0570.995195.2
4.2-403.70.0480.996192.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O33

3o33


Resolution: 1.951→31.399 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 22.93
RfactorNum. reflection% reflection
Rfree0.2204 2680 5.1 %
Rwork0.1771 --
obs0.1794 52544 92.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.55 Å2 / Biso mean: 36.6442 Å2 / Biso min: 14.29 Å2
Refinement stepCycle: final / Resolution: 1.951→31.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3831 0 1937 242 6010
Biso mean--43.33 36.13 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085893
X-RAY DIFFRACTIONf_angle_d0.867981
X-RAY DIFFRACTIONf_chiral_restr0.05852
X-RAY DIFFRACTIONf_plane_restr0.0051029
X-RAY DIFFRACTIONf_dihedral_angle_d13.2723592
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.951-1.98650.26841240.22372564268891
1.9865-2.02470.26051310.20292661279290
2.0247-2.0660.241290.20692365249486
2.066-2.11090.26311390.19392685282493
2.1109-2.160.24521450.19422721286695
2.16-2.2140.22411520.18472617276993
2.214-2.27380.25281330.19322661279494
2.2738-2.34070.25551520.18922607275993
2.3407-2.41630.25441400.18562633277392
2.4163-2.50260.2461410.18772466260788
2.5026-2.60270.23191360.19352712284895
2.6027-2.72110.25431350.18562721285694
2.7211-2.86450.241610.19032666282794
2.8645-3.04380.24821320.20062669280193
3.0438-3.27860.22321350.18932464259988
3.2786-3.60810.23561450.17242724286996
3.6081-4.12920.18381520.15522717286995
4.1292-5.19860.18661430.14872571271491
5.1986-31.40310.18721550.16372640279593
Refinement TLS params.Method: refined / Origin x: 0.6662 Å / Origin y: -0.2955 Å / Origin z: 0.1867 Å
111213212223313233
T0.189 Å20.0053 Å2-0.0076 Å2-0.1409 Å2-0.0055 Å2--0.1993 Å2
L0.1875 °20.0244 °2-0.0661 °2-0.0007 °20.042 °2--0.3672 °2
S0.0479 Å °-0.0023 Å °0.0201 Å °-0.0025 Å °-0.036 Å °0.0073 Å °0.0266 Å °0.0126 Å °-0.01 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allE2 - 5
2X-RAY DIFFRACTION1allF1 - 259
3X-RAY DIFFRACTION1allA1 - 881
4X-RAY DIFFRACTION1allA892 - 1006
5X-RAY DIFFRACTION1allB1 - 886
6X-RAY DIFFRACTION1allB890 - 1006
7X-RAY DIFFRACTION1allC1 - 885
8X-RAY DIFFRACTION1allC891 - 1006
9X-RAY DIFFRACTION1allD1 - 881
10X-RAY DIFFRACTION1allD892 - 1006
11X-RAY DIFFRACTION1allG1
12X-RAY DIFFRACTION1allG2

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