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- PDB-5yj8: Identification of a small molecule inhibitor for the Tudor domain... -

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Basic information

Entry
Database: PDB / ID: 5yj8
TitleIdentification of a small molecule inhibitor for the Tudor domain of TDRD3
ComponentsTudor domain-containing protein 3
KeywordsTRANSCRIPTION/INHIBITOR / Transcriptional coactivator / complex / inhibitor / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


DNA topoisomerase III-beta-TDRD3 complex / DNA topological change / methylated histone binding / chromatin organization / transcription coactivator activity / chromatin binding / Golgi apparatus / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Tudor domain-containing protein 3, UBA domain / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / Tudor domain / Tudor domain profile. / UBA/TS-N domain / Tudor domain / Tudor domain ...: / Tudor domain-containing protein 3, UBA domain / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / Tudor domain / Tudor domain profile. / UBA/TS-N domain / Tudor domain / Tudor domain / Ubiquitin associated domain / SH3 type barrels. - #140 / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
5-(aminomethyl)-1,3-dimethyl-benzimidazol-2-one / Tudor domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.762 Å
AuthorsLiu, J. / Ruan, K.
CitationJournal: FEBS J. / Year: 2018
Title: Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit.
Authors: Liu, J. / Zhang, S. / Liu, M. / Liu, Y. / Nshogoza, G. / Gao, J. / Ma, R. / Yang, Y. / Wu, J. / Zhang, J. / Li, F. / Ruan, K.
History
DepositionOct 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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: Tudor domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4343
Polymers7,1471
Non-polymers2872
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area4430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.974, 50.974, 42.087
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-702-

SO4

21A-837-

HOH

31A-838-

HOH

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Components

#1: Protein Tudor domain-containing protein 3


Mass: 7147.088 Da / Num. of mol.: 1 / Fragment: Tudor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDRD3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q9H7E2
#2: Chemical ChemComp-8W9 / 5-(aminomethyl)-1,3-dimethyl-benzimidazol-2-one


Mass: 191.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N3O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.5M Ammonium sulfate, 0.1M Sodium acetate trihydrate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.76→40 Å / Num. obs: 6495 / % possible obs: 99.4 % / Redundancy: 19 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.018 / Rrim(I) all: 0.078 / Χ2: 1.054 / Net I/σ(I): 4.5 / Num. measured all: 123251
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.7915.70.5042950.970.1270.520.45596.1
1.79-1.8218.20.4583230.9780.1080.4710.45899.4
1.82-1.8619.10.413140.9140.0960.4210.58998.7
1.86-1.919.90.3523200.980.080.3610.541100
1.9-1.9419.60.3043200.9850.0690.3120.54598.2
1.94-1.9819.50.2433070.9930.0560.2490.483100
1.98-2.0318.40.1953240.9930.0460.20.52799.1
2.03-2.0918.90.1783200.9080.0430.1830.588100
2.09-2.1520.30.173180.9940.0380.1740.5199.1
2.15-2.2220.10.1523340.9950.0340.1560.45799.1
2.22-2.319.90.1273090.9970.0290.130.457100
2.3-2.3918.90.1233280.9770.0290.1271.23599.7
2.39-2.518.40.1073210.9920.0260.1111.02399.7
2.5-2.6319.30.13310.9880.0230.1031.05999.7
2.63-2.7919.90.0773250.9980.0170.0790.429100
2.79-3.0119.90.0713320.9890.0160.0731.30699.7
3.01-3.31180.0593260.9960.0140.0611.075100
3.31-3.7919.80.0623350.9830.0140.0642.993100
3.79-4.7718.40.0463390.9990.0110.0472.101100
4.77-4017.40.0553740.9910.0140.0573.833100

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PMT

3pmt


Resolution: 1.762→30.462 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 635 9.8 %
Rwork0.1866 --
obs0.1906 6480 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.76 Å2 / Biso mean: 26.5879 Å2 / Biso min: 16.25 Å2
Refinement stepCycle: final / Resolution: 1.762→30.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms504 0 19 38 561
Biso mean--29.5 31.96 -
Num. residues----60
LS refinement shellResolution: 1.7621→1.8982 Å /
RfactorNum. reflection
Rfree0.2248 132
Rwork0.1876 1227
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)Origin x (Å)Origin y (Å)Origin z (Å)
13.6418-3.51040.95933.4288-1.19631.87320.1102-0.16520.2561-0.0123-0.1323-0.35520.01360.1990.05820.2014-0.0274-0.0010.24650.01870.1632-26.255925.19951.4155
28.9411.06691.66762.1397-0.01683.7759-0.28190.45650.5681-0.04980.1589-0.1753-0.15530.54530.10460.20990.00580.03570.28130.00670.2138-8.652717.56722.6664
37.8424-2.0991-1.54233.23430.8964.876-0.12010.38990.1092-0.0466-0.0966-0.03990.1293-0.01050.18510.2059-0.0099-0.02680.2351-0.00010.1846-16.171415.43415.5858
43.0611-1.12582.87814.0293-0.62183.1875-0.18990.24970.46870.1259-0.1224-0.2124-0.23450.21850.33050.18050.010.0190.23970.00040.3085-15.236819.01614.9429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 549 through 560 )A549 - 560
2X-RAY DIFFRACTION2chain 'A' and (resid 561 through 570 )A561 - 570
3X-RAY DIFFRACTION3chain 'A' and (resid 571 through 595 )A571 - 595
4X-RAY DIFFRACTION4chain 'A' and (resid 596 through 608 )A596 - 608

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