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- PDB-5h1v: Complex structure of TRIM24 PHD-bromodomain and inhibitor 6 -

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Basic information

Entry
Database: PDB / ID: 5h1v
TitleComplex structure of TRIM24 PHD-bromodomain and inhibitor 6
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 / 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
2-Hydrazino-1,3-benzothiazole-6-carbohydrazide / Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2499
Polymers42,4632
Non-polymers7867
Water2,576143
1
A: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6645
Polymers21,2311
Non-polymers4324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5854
Polymers21,2311
Non-polymers3543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.028, 36.027, 113.207
Angle α, β, γ (deg.)90.000, 96.880, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-7FU / 2-Hydrazino-1,3-benzothiazole-6-carbohydrazide


Mass: 223.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9N5OS
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
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: Mar 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 27040 / % possible obs: 98.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 26.42 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.041 / Rrim(I) all: 0.09 / Χ2: 0.931 / Net I/av σ(I): 19.897 / Net I/σ(I): 6.5 / Num. measured all: 126161
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.074.70.39726260.9260.2020.4470.62598.6
2.07-2.154.50.29826660.940.1560.3380.58198.3
2.15-2.254.50.24526840.9450.1290.2780.75998.2
2.25-2.374.80.18127300.9760.0910.2040.67299.7
2.37-2.524.80.13926800.9850.0710.1570.70499.1
2.52-2.714.70.1126910.9880.0560.1240.77798.6
2.71-2.994.60.08526780.9920.0440.0960.93398
2.99-3.424.90.06927500.9940.0350.0781.19199.4
3.42-4.314.50.05626910.9960.0290.0641.50197.2
4.31-404.60.05328440.9970.0270.061.53598.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H1T

5h1t


Resolution: 2.002→37.464 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 1359 5.03 %
Rwork0.1804 25650 -
obs0.1825 27009 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.54 Å2 / Biso mean: 34.8989 Å2 / Biso min: 14.22 Å2
Refinement stepCycle: final / Resolution: 2.002→37.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 44 143 2947
Biso mean--51.2 35.67 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062861
X-RAY DIFFRACTIONf_angle_d0.7573868
X-RAY DIFFRACTIONf_chiral_restr0.047415
X-RAY DIFFRACTIONf_plane_restr0.005496
X-RAY DIFFRACTIONf_dihedral_angle_d12.911737
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0021-2.07360.24521120.17792451256396
2.0736-2.15660.25171380.18752528266698
2.1566-2.25480.25271350.18782549268498
2.2548-2.37360.23171260.186326182744100
2.3736-2.52230.2571400.18462545268599
2.5223-2.7170.23881240.19952566269099
2.717-2.99030.2641350.20642566270198
2.9903-3.42280.24161670.19882580274799
3.4228-4.31130.18071400.1582560270097
4.3113-37.47040.18541420.16522687282998
Refinement TLS params.Method: refined / Origin x: 13.2478 Å / Origin y: -0.6278 Å / Origin z: 13.045 Å
111213212223313233
T0.158 Å20.0035 Å20.0407 Å2-0.1431 Å2-0.012 Å2--0.2219 Å2
L0.2298 °20.0113 °20.2981 °2-0.4077 °20.0926 °2--1.3619 °2
S-0.0083 Å °-0.0324 Å °0.0123 Å °0.0967 Å °0.0247 Å °0.0289 Å °-0.0261 Å °-0.0258 Å °-0.0144 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA825 - 1006
2X-RAY DIFFRACTION1allB825 - 1006
3X-RAY DIFFRACTION1allC1 - 4
4X-RAY DIFFRACTION1allD0 - 1
5X-RAY DIFFRACTION1allF1 - 54
6X-RAY DIFFRACTION1allF55 - 155
7X-RAY DIFFRACTION1allE2

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