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- PDB-5gve: Human TOP3B-TDRD3 complex -

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Basic information

Entry
Database: PDB / ID: 5gve
TitleHuman TOP3B-TDRD3 complex
Components
  • DNA topoisomerase 3-beta-1
  • Tudor domain-containing protein 3
KeywordsISOMERASE/PROTEIN BINDING / Topoisomerase / scaffold / ISOMERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


DNA topoisomerase III-beta-TDRD3 complex / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / condensed chromosome / methylated histone binding / chromosome segregation / chromatin organization / transcription coactivator activity ...DNA topoisomerase III-beta-TDRD3 complex / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / condensed chromosome / methylated histone binding / chromosome segregation / chromatin organization / transcription coactivator activity / chromatin binding / Golgi apparatus / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Tudor domain-containing protein 3, UBA domain / DNA topoisomerase 3-like, TOPRIM 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 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 ...: / Tudor domain-containing protein 3, UBA domain / DNA topoisomerase 3-like, TOPRIM 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 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / Tudor domain / Tudor domain profile. / TOPRIM / UBA/TS-N domain / Tudor domain / Tudor domain / Ubiquitin associated domain / Toprim domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Toprim domain profile. / TOPRIM domain / UBA-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA topoisomerase 3-beta-1 / Tudor domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.606 Å
AuthorsGoto-Ito, S. / Yamagata, A. / Sato, Y. / Takahashi, T.S. / Fukai, S.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Authors: Goto-Ito, S. / Yamagata, A. / Takahashi, T.S. / Sato, Y. / Fukai, S.
History
DepositionSep 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 3-beta-1
B: Tudor domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9673
Polymers86,9422
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-17 kcal/mol
Surface area37820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.563, 173.563, 111.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein DNA topoisomerase 3-beta-1 / DNA topoisomerase III beta-1


Mass: 69163.969 Da / Num. of mol.: 1 / Fragment: UNP residues 1-612
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP3B, TOP3B1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O95985, DNA topoisomerase
#2: Protein Tudor domain-containing protein 3


Mass: 17778.318 Da / Num. of mol.: 1 / Fragment: UNP residues 1-161
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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 5.59 Å3/Da / Density % sol: 78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 50 mM Na-cacodylate, 10 mM MgSO4, 1.7 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 22224 / % possible obs: 99.9 % / Redundancy: 9 % / Net I/σ(I): 11.2
Reflection shellResolution: 3.6→3.66 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GVC, 5GVD

5gvc

5gvd


Resolution: 3.606→46.997 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.92
RfactorNum. reflection% reflection
Rfree0.2452 1134 5.11 %
Rwork0.1981 --
obs0.2004 22208 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.606→46.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 1 0 6083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046208
X-RAY DIFFRACTIONf_angle_d1.1358399
X-RAY DIFFRACTIONf_dihedral_angle_d13.5162325
X-RAY DIFFRACTIONf_chiral_restr0.079938
X-RAY DIFFRACTIONf_plane_restr0.0041087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6057-3.76980.33531350.27192625X-RAY DIFFRACTION100
3.7698-3.96840.28761430.24112608X-RAY DIFFRACTION100
3.9684-4.21690.25821480.21042620X-RAY DIFFRACTION100
4.2169-4.54230.20931370.17052609X-RAY DIFFRACTION100
4.5423-4.99890.22441420.1762639X-RAY DIFFRACTION100
4.9989-5.72120.29131520.19772624X-RAY DIFFRACTION100
5.7212-7.20390.28391450.222646X-RAY DIFFRACTION100
7.2039-47.00120.19821320.17872703X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -22.0221 Å / Origin y: -51.7221 Å / Origin z: 0.4102 Å
111213212223313233
T1.5584 Å2-0.5168 Å20.112 Å2-1.0689 Å2-0.003 Å2--1.1073 Å2
L0.777 °20.922 °21.2205 °2-1.4405 °21.6754 °2--1.6832 °2
S-0.1472 Å °0.3326 Å °-0.0442 Å °-0.2489 Å °0.278 Å °-0.0259 Å °0.3492 Å °-0.0163 Å °-0.1279 Å °
Refinement TLS groupSelection details: all

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