[English] 日本語
Yorodumi
- PDB-5gvc: Human Topoisomerase IIIb topo domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gvc
TitleHuman Topoisomerase IIIb topo domain
ComponentsDNA topoisomerase 3-beta-1
KeywordsISOMERASE / Topoisomerase
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 / chromosome segregation / DNA recombination / DNA repair / DNA binding ...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 / chromosome segregation / DNA recombination / DNA repair / DNA binding / RNA binding / nucleus
Similarity search - Function
DNA topoisomerase 3-like, TOPRIM 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 3-like, TOPRIM 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. / Topoisomerase (Topo) IA-type catalytic domain profile. / 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 / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA topoisomerase 3-beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.436 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase 3-beta-1
B: DNA topoisomerase 3-beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6854
Polymers138,6362
Non-polymers492
Water7,404411
1
A: DNA topoisomerase 3-beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3422
Polymers69,3181
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area29000 Å2
MethodPISA
2
B: DNA topoisomerase 3-beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3422
Polymers69,3181
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.088, 93.665, 91.608
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 69318.133 Da / Num. of mol.: 2 / 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, EC: 5.99.1.2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES-Na, 0.2 M MgCl2, 25% PEG3350

-
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 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 55090 / % possible obs: 99.1 % / Redundancy: 6.7 % / Net I/σ(I): 13.4
Reflection shellResolution: 2.44→2.48 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CGY

4cgy


Resolution: 2.436→49.718 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 2793 5.07 %
Rwork0.182 --
obs0.1844 55088 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.436→49.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9591 0 2 411 10004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029800
X-RAY DIFFRACTIONf_angle_d0.68513254
X-RAY DIFFRACTIONf_dihedral_angle_d12.5943669
X-RAY DIFFRACTIONf_chiral_restr0.0251467
X-RAY DIFFRACTIONf_plane_restr0.0031714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4357-2.47770.29681360.23912406X-RAY DIFFRACTION91
2.4777-2.52270.31891320.24342617X-RAY DIFFRACTION100
2.5227-2.57120.30221420.23332635X-RAY DIFFRACTION100
2.5712-2.62370.28711280.22522629X-RAY DIFFRACTION99
2.6237-2.68080.27081500.21782631X-RAY DIFFRACTION99
2.6808-2.74310.28251280.20992594X-RAY DIFFRACTION99
2.7431-2.81170.26881330.21792595X-RAY DIFFRACTION99
2.8117-2.88770.24991310.2172592X-RAY DIFFRACTION98
2.8877-2.97270.26431550.22052629X-RAY DIFFRACTION100
2.9727-3.06860.28621390.2252625X-RAY DIFFRACTION100
3.0686-3.17830.32171590.22752609X-RAY DIFFRACTION99
3.1783-3.30550.26031400.21662616X-RAY DIFFRACTION99
3.3055-3.45590.27011500.1982605X-RAY DIFFRACTION99
3.4559-3.63810.20491380.17952593X-RAY DIFFRACTION98
3.6381-3.86590.22191320.16822645X-RAY DIFFRACTION100
3.8659-4.16430.19911450.15452661X-RAY DIFFRACTION99
4.1643-4.58310.16711320.1362617X-RAY DIFFRACTION99
4.5831-5.24560.191550.14462629X-RAY DIFFRACTION99
5.2456-6.60650.20451400.15862660X-RAY DIFFRACTION99
6.6065-49.72820.14171280.13752707X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 23.4613 Å / Origin y: 17.4944 Å / Origin z: -15.61 Å
111213212223313233
T0.224 Å2-0.0133 Å2-0.0009 Å2-0.262 Å2-0.0028 Å2--0.2819 Å2
L0.0532 °2-0.1396 °20.0618 °2-0.3285 °2-0.1926 °2--0.2219 °2
S0.0207 Å °0.0168 Å °-0.015 Å °0.0001 Å °-0.0081 Å °0.0856 Å °0.0079 Å °-0.0227 Å °-0.0105 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more