[English] 日本語
Yorodumi
- PDB-7kte: DNA Polymerase Mu, 8-oxodGTP:Ct Reaction State Ternary Complex, 5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kte
TitleDNA Polymerase Mu, 8-oxodGTP:Ct Reaction State Ternary Complex, 50 mM Mg2+ (90min)
Components
  • DNA (5'-D(*CP*GP*GP*CP*CP*TP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA-directed DNA/RNA polymerase mu
KeywordsREPLICATION / Time-Lapse Crystallography / Oxidized Nucleotide Insertion / DNA Polymerase Mu / Double Strand Break Repair
Function / homology
Function and homology information


Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / DNA polymerase beta, palm domain / DNA polymerase beta palm / 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-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / DNA polymerase beta, palm domain / DNA polymerase beta palm / 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, thumb domain superfamily / DNA polymerase beta thumb / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / PYROPHOSPHATE / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.479 Å
AuthorsJamsen, J.A. / Wilson, S.H.
Funding support United States, Japan, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050158 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050161 United States
Japan Society for the Promotion of Science (JSPS)16K16195 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide.
Authors: Jamsen, J.A. / Sassa, A. / Shock, D.D. / Beard, W.A. / Wilson, S.H.
History
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed DNA/RNA polymerase mu
T: DNA (5'-D(*CP*GP*GP*CP*CP*TP*AP*CP*G)-3')
P: DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,22620
Polymers45,4994
Non-polymers1,72716
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-52 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.940, 68.523, 110.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA-directed DNA/RNA polymerase mu / Pol Mu / Terminal transferase


Mass: 40054.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Plasmid: pGEXM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NP87, DNA-directed DNA polymerase

-
DNA chain , 3 types, 3 molecules TPD

#2: DNA chain DNA (5'-D(*CP*GP*GP*CP*CP*TP*AP*CP*G)-3')


Mass: 2716.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')


Mass: 1536.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*GP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 10 types, 466 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-8DG / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#12: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#13: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.72 % / Mosaicity: 0.197 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 85-90mM HEPES pH 7.5, 17-18% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.479→50 Å / Num. obs: 76692 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.06 / Rrim(I) all: 0.149 / Χ2: 1.157 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.48-1.515.90.88637580.690.3970.9741.05799.9
1.51-1.536.10.78938060.7730.3460.8631.099100
1.53-1.566.20.6837740.8110.2960.7431.12699.9
1.56-1.596.20.58838060.8550.2580.6441.13199.8
1.59-1.6360.48237950.8910.2130.5281.206100
1.63-1.675.60.38537870.9280.1780.4251.19899.9
1.67-1.715.80.33637620.9360.1510.3691.20999.7
1.71-1.756.60.338180.9570.1270.3261.212100
1.75-1.816.70.25938120.9650.1090.2811.201100
1.81-1.866.60.21938010.9710.0920.2381.191100
1.86-1.936.50.19238050.9770.0810.2091.211100
1.93-2.016.40.17138220.9760.0730.1861.226100
2.01-2.16.30.15338180.9780.0670.1671.188100
2.1-2.2160.13938560.9770.0620.1521.178100
2.21-2.355.40.12538170.9770.0590.1391.10699.8
2.35-2.536.40.12538490.9790.0540.1361.1599.9
2.53-2.796.80.12538550.980.0520.1351.186100
2.79-3.196.60.12239070.9820.0520.1331.101100
3.19-4.026.10.11739370.9810.0520.1291.054100
4.02-505.80.12241070.9730.0560.1341.08399.4

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.15.2-3472refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M04

4m04


Resolution: 1.479→34.958 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1774 3831 5 %
Rwork0.1568 72786 -
obs0.1578 76617 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.7 Å2 / Biso mean: 23.8562 Å2 / Biso min: 10.34 Å2
Refinement stepCycle: final / Resolution: 1.479→34.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 365 81 460 3468
Biso mean--33.33 34.85 -
Num. residues----346
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4794-1.49810.26521410.2494266199
1.4981-1.51780.24141380.23082641100
1.5178-1.53860.24181410.22122653100
1.5386-1.56060.21571390.19942652100
1.5606-1.58390.20991400.19122656100
1.5839-1.60860.21151420.182691100
1.6086-1.6350.19061390.17992639100
1.635-1.66320.20721420.172718100
1.6632-1.69350.19531380.16712622100
1.6935-1.7260.1871410.16442694100
1.726-1.76130.18411420.16412675100
1.7613-1.79950.20521390.16152657100
1.7995-1.84140.17161420.16222686100
1.8414-1.88750.20841400.15562677100
1.8875-1.93850.18561400.15872714100
1.9385-1.99550.16731440.15372664100
1.9955-2.05990.21271400.15492690100
2.0599-2.13350.17641430.14612705100
2.1335-2.21890.17491420.14372695100
2.2189-2.31990.16791400.14422684100
2.3199-2.44220.1641440.13742691100
2.4422-2.59520.1481430.14482731100
2.5952-2.79550.16931440.14592707100
2.7955-3.07660.1551440.15452738100
3.0766-3.52150.15311440.14532765100
3.5215-4.43520.14781450.13962775100
4.4352-34.9580.2161540.18162905100
Refinement TLS params.Method: refined / Origin x: 2.9052 Å / Origin y: -4.21 Å / Origin z: -11.441 Å
111213212223313233
T0.125 Å20.0044 Å2-0.0055 Å2-0.1286 Å20.0106 Å2--0.1028 Å2
L0.8924 °2-0.1725 °2-0.1312 °2-0.7736 °20.0805 °2--0.577 °2
S0.0328 Å °0.0979 Å °0.0406 Å °-0.0466 Å °-0.0239 Å °-0.0364 Å °0.0111 Å °0.0186 Å °0.0011 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA137 - 494
2X-RAY DIFFRACTION1allT1 - 9
3X-RAY DIFFRACTION1allP1 - 5
4X-RAY DIFFRACTION1allD1 - 4
5X-RAY DIFFRACTION1allB1 - 2
6X-RAY DIFFRACTION1allI1
7X-RAY DIFFRACTION1allK1
8X-RAY DIFFRACTION1allG1
9X-RAY DIFFRACTION1allC1
10X-RAY DIFFRACTION1allE1
11X-RAY DIFFRACTION1allF1 - 8
12X-RAY DIFFRACTION1allJ1
13X-RAY DIFFRACTION1allH1
14X-RAY DIFFRACTION1allS1 - 518

+
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