[English] 日本語
Yorodumi
- EMDB-43855: Ternary complex of human DNA polymerase theta polymerase domain w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43855
TitleTernary complex of human DNA polymerase theta polymerase domain with a cognate C:G base pair
Map dataTernary complex of human DNA polymerase theta polymerase domain with a cognate C:G base pair
Sample
  • Complex: Ternary complex of human DNA polymerase theta polymerase domain with a cognate C:G base pair
    • Protein or peptide: DNA polymerase theta
    • DNA: DNA (5'-D(*AP*GP*CP*TP*CP*TP*AP*CP*GP*GP*AP*TP*GP*C)-3')
    • DNA: DNA (5'-D(P*GP*CP*AP*TP*CP*CP*GP*TP*AP*GP*(2DA))-3')
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsDNA translesion synthesis / theta-mediated end joining / A-family DNA polymerase / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / replication fork processing / site of DNA damage / mitochondrial nucleoid / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination ...double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / replication fork processing / site of DNA damage / mitochondrial nucleoid / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / RNA-directed DNA polymerase activity / DNA helicase activity / base-excision repair / protein homooligomerization / RNA-directed DNA polymerase / double-strand break repair / site of double-strand break / DNA helicase / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / chromatin binding / magnesium ion binding / Golgi apparatus / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
: / DNA_pol_Q helicase like region helical domain / DNA polymerase theta-like, helix-turn-helix domain / Helix-turn-helix domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain ...: / DNA_pol_Q helicase like region helical domain / DNA polymerase theta-like, helix-turn-helix domain / Helix-turn-helix domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA polymerase theta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsLi C / Gao Y
Funding support United States, 2 items
OrganizationGrant numberCountry
American Cancer SocietyRSG-22-082-517 01-DMC United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR190046 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of error-prone DNA synthesis by DNA polymerase θ.
Authors: Chuxuan Li / Leora M Maksoud / Yang Gao /
Abstract: DNA polymerase θ (Pol θ) is an A-family DNA polymerase specialized in DNA double-strand breaks repair and translesion synthesis. Distinct from its high-fidelity homologs in DNA replication, Pol θ ...DNA polymerase θ (Pol θ) is an A-family DNA polymerase specialized in DNA double-strand breaks repair and translesion synthesis. Distinct from its high-fidelity homologs in DNA replication, Pol θ catalyzes template-dependent DNA synthesis with an inherent propensity for error incorporation. However, the structural basis of Pol θ's low-fidelity DNA synthesis is not clear. Here, we present cryo-electron microscopy structures detailing the polymerase domain of human Pol θ in complex with a cognate C:G base pair (bp), a mismatched T:G bp, or a mismatched T:T bp. Our structures illustrate that Pol θ snugly accommodates the mismatched nascent base pairs within its active site with the finger domain well-closed, consistent with our in-solution fluorescence measurement but in contrast to its high-fidelity homologs. In addition, structural examination and mutagenesis study show that unique residues surrounding the active site contribute to the stabilization of the mismatched nascent base pair. Furthermore, Pol θ can efficiently extend from the misincorporated T:G or T:T mismatches, yet with a preference for template or primer looping-out, resulting in insertions and deletions. Collectively, our results elucidate how an A-family polymerase is adapted for error-prone DNA synthesis.
History
DepositionFeb 28, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43855.png

Downloads & links

-
Map

FileDownload / File: emd_43855.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTernary complex of human DNA polymerase theta polymerase domain with a cognate C:G base pair
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.236
Minimum - Maximum-1.6530921 - 2.4623668
Average (Standard dev.)-0.0005469664 (±0.047926713)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map A

Fileemd_43855_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43855_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of human DNA polymerase theta polymerase domain w...

EntireName: Ternary complex of human DNA polymerase theta polymerase domain with a cognate C:G base pair
Components
  • Complex: Ternary complex of human DNA polymerase theta polymerase domain with a cognate C:G base pair
    • Protein or peptide: DNA polymerase theta
    • DNA: DNA (5'-D(*AP*GP*CP*TP*CP*TP*AP*CP*GP*GP*AP*TP*GP*C)-3')
    • DNA: DNA (5'-D(P*GP*CP*AP*TP*CP*CP*GP*TP*AP*GP*(2DA))-3')
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Ternary complex of human DNA polymerase theta polymerase domain w...

SupramoleculeName: Ternary complex of human DNA polymerase theta polymerase domain with a cognate C:G base pair
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: DNA polymerase theta

MacromoleculeName: DNA polymerase theta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.585555 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: GFKDNSPISD TSFSLQLSQD GLQLTPASSS SESLSIIDVA SDQNLFQTFI KEWRCKKRFS ISLACEKIRS LTSSKTATIG SRFKQASSP QEIPIRDDGF PIKGCDDTLV VGLAVCWGGR DAYYFSLQKE QKHSEISASL VPPSLDPSLT LKDRMWYLQS C LRKESDKE ...String:
GFKDNSPISD TSFSLQLSQD GLQLTPASSS SESLSIIDVA SDQNLFQTFI KEWRCKKRFS ISLACEKIRS LTSSKTATIG SRFKQASSP QEIPIRDDGF PIKGCDDTLV VGLAVCWGGR DAYYFSLQKE QKHSEISASL VPPSLDPSLT LKDRMWYLQS C LRKESDKE CSVVIYDFIQ SYKILLLSCG ISLEQSYEDP KVACWLLDPD SQEPTLHSIV TSFLPHELPL LEGMETSQGI QS LGLNAGS EHSGRYRASV ESILIFNSMN QLNSLLQKEN LQDVFRKVEM PSQYCLALLE LNGIGFSTAE CESQKHIMQA KLD AIETQA YQLAGHSFSF TSSDDIAEVL FLELKLPPNR EMKNQGSKKT LGSTRRGIDN GRKLRLGRQF STSKDVLNKL KALH PLPGL ILEWRRITNA ITKVVFPLQR EKCLNPFLGM ERIYPVSQSH TATGRITFTE PNIQNVPRDF EIKMPTLVGE SPPSQ AVGK GLLPMGRGKY KKGFSVNPRC QAQMEERAAD RGMPFSISMR HAFVPFPGGS ILAADYSQLE LRILAHLSHD RRLIQV LNT GADVFRSIAA EWKMIEPESV GDDLRQQAKQ ICYGIIYGMG AKSLGEQMGI KENDAACYID SFKSRYTGIN QFMTETV KN CKRDGFVQTI LGRRRYLPGI KDNNPYRKAH AERQAINTIV QGSAADIVKI ATVNIQKQLE TFHSTFKSHG HREGMLQS D QTGLSRKRKL QGMFCPIRGG FFILQLHDEL LYEVAEEDVV QVAQIVKNEM ESAVKLSVKL KVKVKIGASW GELKDFDV

UniProtKB: DNA polymerase theta

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

MacromoleculeName: DNA (5'-D(*AP*GP*CP*TP*CP*TP*AP*CP*GP*GP*AP*TP*GP*C)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.864712 KDa
SequenceString:
(DG)(DC)(DA)(DG)(DT)(DC)(DA)(DG)(DC)(DT) (DC)(DT)(DA)(DC)(DG)(DG)(DA)(DT)(DG)(DC) (DC)(DT)(DC)(DA)(DC)(DA)(DG)(DC)(DA)

-
Macromolecule #3: DNA (5'-D(P*GP*CP*AP*TP*CP*CP*GP*TP*AP*GP*(2DA))-3')

MacromoleculeName: DNA (5'-D(P*GP*CP*AP*TP*CP*CP*GP*TP*AP*GP*(2DA))-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.174001 KDa
SequenceString:
(DT)(DG)(DC)(DT)(DG)(DT)(DG)(DA)(DG)(DG) (DC)(DA)(DT)(DC)(DC)(DG)(DT)(DA)(DG) (2DA)

-
Macromolecule #4: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: DGT
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.6
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 231192
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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