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- PDB-6v9t: Tudor domain of TDRD3 in complex with a small molecule -

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Basic information

Entry
Database: PDB / ID: 6v9t
TitleTudor domain of TDRD3 in complex with a small molecule
ComponentsTudor domain-containing protein 3
KeywordsTRANSFERASE / structural genomics consortium / SGC
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 / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily
Similarity search - Domain/homology
Chem-36X / Tudor domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.154 Å
AuthorsLi, W. / Tempel, W. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2022
Title: A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II.
Authors: Liu, Y. / Iqbal, A. / Li, W. / Ni, Z. / Wang, Y. / Ramprasad, J. / Abraham, K.J. / Zhang, M. / Zhao, D.Y. / Qin, S. / Loppnau, P. / Jiang, H. / Guo, X. / Brown, P.J. / Zhen, X. / Xu, G. / ...Authors: Liu, Y. / Iqbal, A. / Li, W. / Ni, Z. / Wang, Y. / Ramprasad, J. / Abraham, K.J. / Zhang, M. / Zhao, D.Y. / Qin, S. / Loppnau, P. / Jiang, H. / Guo, X. / Brown, P.J. / Zhen, X. / Xu, G. / Mekhail, K. / Ji, X. / Bedford, M.T. / Greenblatt, J.F. / Min, J.
History
DepositionDec 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Tudor domain-containing protein 3
BBB: Tudor domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5918
Polymers18,0262
Non-polymers5656
Water19811
1
AAA: Tudor domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3904
Polymers9,0131
Non-polymers3773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: Tudor domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2014
Polymers9,0131
Non-polymers1883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.855, 83.855, 114.045
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11BBB-703-

UNX

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Components

#1: Protein Tudor domain-containing protein 3


Mass: 9013.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDRD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H7E2
#2: Chemical ChemComp-36X / 4-methyl-2,3,4,5,6,7-hexahydrodicyclopenta[b,e]pyridin-8(1H)-imine


Mass: 188.269 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H16N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.2 M sodium citrate, 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.15→44.85 Å / Num. obs: 8558 / % possible obs: 99.8 % / Redundancy: 11.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.109 / Net I/σ(I): 18.9
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
8.88-44.8599.39.10.0471410.9990.0553.7
2.15-2.229811.10.9827030.8841.032.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3pmt

3pmt


Resolution: 2.154→44.849 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 11.506 / SU ML: 0.142 / Cross valid method: FREE R-VALUE / ESU R: 0.212 / ESU R Free: 0.177 / Details: Thin shell selection of free reflections (SFTOOLS)
RfactorNum. reflection% reflection
Rfree0.2289 699 8.169 %
Rwork0.1955 --
all0.198 --
obs-8557 99.837 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20.495 Å2-0 Å2
2--0.99 Å2-0 Å2
3----3.21 Å2
Refinement stepCycle: LAST / Resolution: 2.154→44.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 45 11 924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.013983
X-RAY DIFFRACTIONr_bond_other_d0.0020.017857
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.6871351
X-RAY DIFFRACTIONr_angle_other_deg1.4111.7141982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6075111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9642542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97815134
X-RAY DIFFRACTIONr_chiral_restr0.0990.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02213
X-RAY DIFFRACTIONr_nbd_refined0.1870.2158
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.2699
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2437
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.2417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.29
X-RAY DIFFRACTIONr_nbd_other0.1840.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3330.23
X-RAY DIFFRACTIONr_mcbond_it3.3823.304445
X-RAY DIFFRACTIONr_mcbond_other3.3793.305446
X-RAY DIFFRACTIONr_mcangle_it4.3984.912548
X-RAY DIFFRACTIONr_mcangle_other4.3944.914549
X-RAY DIFFRACTIONr_scbond_it3.8883.769538
X-RAY DIFFRACTIONr_scbond_other3.8853.77539
X-RAY DIFFRACTIONr_scangle_it5.3855.553802
X-RAY DIFFRACTIONr_scangle_other5.3815.554803
X-RAY DIFFRACTIONr_lrange_it7.14237.3411000
X-RAY DIFFRACTIONr_lrange_other7.14337.365998
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 freeFsc work% reflection obs (%)WRfactor Rwork
2.154-2.210.294610.245570.2456260.840.83798.7220.217
2.21-2.2700.2566060.2566060.8581000.226
2.27-2.3360.276530.2275270.2315800.8640.8911000.194
2.336-2.4070.255610.2025080.2085690.9030.9111000.172
2.407-2.4860.245520.215120.2135640.8980.9111000.182
2.486-2.5730.34600.2414900.2525500.8560.8891000.212
2.573-2.670.2470.2264760.2235230.9220.911000.191
2.67-2.7780.241390.2194520.2214910.90.9141000.186
2.778-2.9020.293340.1924540.1994880.9150.9341000.166
2.902-3.0430.228350.2014200.2034550.9330.9361000.173
3.043-3.2060.251610.1783760.1884370.930.9481000.156
3.206-3.40.219300.1773940.1814240.9550.9531000.164
3.4-3.6330.198220.183830.1814050.9440.9521000.169
3.633-3.9220.224400.1793210.1843620.9420.95899.72380.175
3.922-4.2930.231200.1513250.1553450.9440.9731000.152
4.293-4.7940.157410.1472660.1483070.9720.9751000.149
4.794-5.5250.198190.1762620.1782810.9520.9671000.179
5.525-6.7420.227130.2322290.2322420.9580.9441000.22
6.742-9.4280.30960.2281830.2311890.940.9521000.239
9.428-44.8490.29450.2951170.2951230.850.92599.1870.353
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)
17.5633-0.05041.32094.3907-1.21226.73550.04050.3449-0.2842-0.2292-0.113-0.27230.22220.29690.07250.03520.01910.01880.0275-0.00290.029482.260114.258534.4464
26.4456-2.21270.29394.9776-0.19414.8160.0607-0.2459-0.11680.13350.02830.3219-0.0483-0.1384-0.0890.0426-0.03690.00340.04530.0090.023468.144311.853949.7698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA554 - 609
2X-RAY DIFFRACTION2ALLBBB555 - 609

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