[English] 日本語
Yorodumi
- PDB-6go4: TdT chimera (Loop1 of pol mu) - binary complex with ddCTP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6go4
TitleTdT chimera (Loop1 of pol mu) - binary complex with ddCTP
ComponentsDNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase
KeywordsDNA BINDING PROTEIN / NHEJ pathway / DNA bridging / DNA polymerase polX
Function / homology
Function and homology information


DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / Nonhomologous End-Joining (NHEJ) / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / somatic hypermutation of immunoglobulin genes / B cell differentiation / euchromatin ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / Nonhomologous End-Joining (NHEJ) / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / somatic hypermutation of immunoglobulin genes / B cell differentiation / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity / chromatin / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain ...DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / breast cancer carboxy-terminal domain / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA nucleotidylexotransferase / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsLoc'h, J. / Gerodimos, C.A. / Rosario, S. / Lieber, M.R. / Delarue, M.
Funding support France, 1items
OrganizationGrant numberCountry
Fondation ARC pour la recherche sur le cancer France
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural evidence for an intransbase selection mechanism involving Loop1 in polymerase mu at an NHEJ double-strand break junction.
Authors: Loc'h, J. / Gerodimos, C.A. / Rosario, S. / Tekpinar, M. / Lieber, M.R. / Delarue, M.
History
DepositionJun 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Jan 17, 2024Group: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3474
Polymers45,8491
Non-polymers4983
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-16 kcal/mol
Surface area17460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.970, 85.620, 114.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase / Terminal addition enzyme / Terminal deoxynucleotidyltransferase / Terminal transferase / Pol Mu / ...Terminal addition enzyme / Terminal deoxynucleotidyltransferase / Terminal transferase / Pol Mu / Terminal transferase / Terminal addition enzyme / Terminal deoxynucleotidyltransferase / Terminal transferase


Mass: 45848.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.,There is an insertion of one residue between loop1 of pol ...Details: There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.,There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.,There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dntt, Tdt, Polm, polmu / Production host: Escherichia coli (E. coli)
References: UniProt: P09838, UniProt: Q9JIW4, DNA nucleotidylexotransferase, DNA-directed DNA polymerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20-24% PEG 6000, 400-800 mM lithium chloride, 100 mM MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.96→47.78 Å / Num. obs: 34181 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Net I/σ(I): 11.02
Reflection shellResolution: 1.96→2.07 Å / Rmerge(I) obs: 1.666 / Num. unique obs: 5333 / CC1/2: 0.498 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JMS

1jms


Resolution: 1.96→47.71 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.175 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1653 5 %RANDOM
Rwork0.201 ---
obs0.203 33047 99.9 %-
Displacement parametersBiso mean: 55.94 Å2
Baniso -1Baniso -2Baniso -3
1-5.9876 Å20 Å20 Å2
2--0.1931 Å20 Å2
3----6.1807 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.96→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 29 359 3203
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012918HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.013947HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1028SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes441HARMONIC5
X-RAY DIFFRACTIONt_it2918HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion16.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion375SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3485SEMIHARMONIC4
LS refinement shellResolution: 1.98→2.04 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.3098 143 5.02 %
Rwork0.2624 2704 -
all0.2648 2847 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -15.1829 Å / Origin y: 12.1982 Å / Origin z: -20.1836 Å
111213212223313233
T-0.2214 Å20.0053 Å20.0075 Å2--0.1909 Å20.0218 Å2--0.0335 Å2
L0.9657 °20.076 °20.0513 °2-1.416 °2-0.7548 °2--1.0233 °2
S0.0045 Å °0.0033 Å °0.0015 Å °-0.0948 Å °-0.095 Å °-0.1368 Å °-0.0617 Å °0.0977 Å °0.0905 Å °
Refinement TLS groupSelection details: { A|* }

+
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://pdbjlvh1.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