[English] 日本語
Yorodumi
- EMDB-52828: Chimeric mitochondrial DNA polymerase gamma ternary complex (hAmB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52828
TitleChimeric mitochondrial DNA polymerase gamma ternary complex (hAmB) in mouse-like error-editing conformer (composite)
Map dataMain map
Sample
  • Complex: Chimeric mitochondrial DNA polymerase gamma ternary complex (hAmB) in mouse-like error-editing conformer (composite)
    • Organelle or cellular component: DNA polymerase subunit gamma-1
      • Protein or peptide: DNA polymerase subunit gamma-1
    • Organelle or cellular component: DNA polymerase subunit gamma-2
      • Protein or peptide: DNA polymerase subunit gamma-2
    • DNA: DNA (primer strand)
    • DNA: DNA (template strand)
  • Ligand: CALCIUM ION
  • Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
KeywordsMitochondrial DNA polymerase / TRANSFERASE
Function / homology
Function and homology information


Strand-asynchronous mitochondrial DNA replication / gamma DNA polymerase complex / mitochondrial chromosome / mitochondrial DNA replication / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA metabolic process / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process ...Strand-asynchronous mitochondrial DNA replication / gamma DNA polymerase complex / mitochondrial chromosome / mitochondrial DNA replication / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA metabolic process / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / DNA polymerase processivity factor activity / mitochondrial nucleoid / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / base-excision repair, gap-filling / DNA polymerase binding / 3'-5' exonuclease activity / mitochondrion organization / base-excision repair / DNA-templated DNA replication / protease binding / double-stranded DNA binding / in utero embryonic development / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / mitochondrial matrix / DNA repair / intracellular membrane-bounded organelle / chromatin binding / protein-containing complex / mitochondrion / DNA binding / identical protein binding
Similarity search - Function
Glycyl-tRNA synthetase-like core domain / DNA-directed DNA-polymerase, family A, mitochondria / DNA mitochondrial polymerase, exonuclease domain / POLG2, C-terminal / : / DNA mitochondrial polymerase exonuclease domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily ...Glycyl-tRNA synthetase-like core domain / DNA-directed DNA-polymerase, family A, mitochondria / DNA mitochondrial polymerase, exonuclease domain / POLG2, C-terminal / : / DNA mitochondrial polymerase exonuclease domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 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 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA polymerase subunit gamma-1 / DNA polymerase subunit gamma-2
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsValenzuela S / Falkenberg M
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Cancerfonden Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Commun / Year: 2025
Title: Modelling POLG mutations in mice unravels a critical role of POLγΒ in regulating phenotypic severity.
Authors: Samantha Corrà / Alessandro Zuppardo / Sebastian Valenzuela / Louise Jenninger / Raffaele Cerutti / Sirelin Sillamaa / Emily Hoberg / Katarina A S Johansson / Urska Rovsnik / Sara Volta / ...Authors: Samantha Corrà / Alessandro Zuppardo / Sebastian Valenzuela / Louise Jenninger / Raffaele Cerutti / Sirelin Sillamaa / Emily Hoberg / Katarina A S Johansson / Urska Rovsnik / Sara Volta / Pedro Silva-Pinheiro / Hannah Davis / Aleksandra Trifunovic / Michal Minczuk / Claes M Gustafsson / Anu Suomalainen / Massimo Zeviani / Bertil Macao / Xuefeng Zhu / Maria Falkenberg / Carlo Viscomi /
Abstract: DNA polymerase γ (POLγ), responsible for mitochondrial DNA replication, consists of a catalytic POLγA subunit and two accessory POLγB subunits. Mutations in POLG, which encodes POLγA, lead to ...DNA polymerase γ (POLγ), responsible for mitochondrial DNA replication, consists of a catalytic POLγA subunit and two accessory POLγB subunits. Mutations in POLG, which encodes POLγA, lead to various mitochondrial diseases. We investigated the most common POLG mutations (A467T, W748S, G848S, Y955C) by characterizing human and mouse POLγ variants. Our data reveal that these mutations significantly impair POLγ activities, with mouse variants exhibiting milder defects. Cryogenic electron microscopy highlighted structural differences between human and mouse POLγ, particularly in the POLγB subunit, which may explain the higher activity of mouse POLγ and the reduced severity of mutations in mice. We further generated a panel of mouse models mirroring common human POLG mutations, providing crucial insights into the pathogenesis of POLG-related disorders and establishing robust models for therapeutic development. Our findings emphasize the importance of POLγB in modulating the severity of POLG mutations.
History
DepositionFeb 14, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52828.png

Downloads & links

-
Map

FileDownload / File: emd_52828.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-30.438026000000001 - 52.253875999999998
Average (Standard dev.)0.16417444 (±0.9165584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Chimeric mitochondrial DNA polymerase gamma ternary complex (hAmB...

EntireName: Chimeric mitochondrial DNA polymerase gamma ternary complex (hAmB) in mouse-like error-editing conformer (composite)
Components
  • Complex: Chimeric mitochondrial DNA polymerase gamma ternary complex (hAmB) in mouse-like error-editing conformer (composite)
    • Organelle or cellular component: DNA polymerase subunit gamma-1
      • Protein or peptide: DNA polymerase subunit gamma-1
    • Organelle or cellular component: DNA polymerase subunit gamma-2
      • Protein or peptide: DNA polymerase subunit gamma-2
    • DNA: DNA (primer strand)
    • DNA: DNA (template strand)
  • Ligand: CALCIUM ION
  • Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

-
Supramolecule #1: Chimeric mitochondrial DNA polymerase gamma ternary complex (hAmB...

SupramoleculeName: Chimeric mitochondrial DNA polymerase gamma ternary complex (hAmB) in mouse-like error-editing conformer (composite)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)

-
Supramolecule #2: DNA polymerase subunit gamma-1

SupramoleculeName: DNA polymerase subunit gamma-1 / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: DNA polymerase subunit gamma-2

SupramoleculeName: DNA polymerase subunit gamma-2 / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: DNA polymerase subunit gamma-1

MacromoleculeName: DNA polymerase subunit gamma-1 / 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: 138.044641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHVSS SVPASDPSDG QRRRQQQQQQ QQQQQQQPQQ PQVLSSEGGQ LRHNPLDIQM LSRGLHEQIF GQGGEMPGEA AVRRSVEHL QKHGLWGQPA VPLPDVELRL PPLYGDNLDQ HFRLLAQKQS LPYLEAANLL LQAQLPPKPP AWAWAEGWTR Y GPEGEAVP ...String:
MHHHHHHVSS SVPASDPSDG QRRRQQQQQQ QQQQQQQPQQ PQVLSSEGGQ LRHNPLDIQM LSRGLHEQIF GQGGEMPGEA AVRRSVEHL QKHGLWGQPA VPLPDVELRL PPLYGDNLDQ HFRLLAQKQS LPYLEAANLL LQAQLPPKPP AWAWAEGWTR Y GPEGEAVP VAIPEERALV FDVEVCLAEG TCPTLAVAIS PSAWYSWCSQ RLVEERYSWT SQLSPADLIP LEVPTGASSP TQ RDWQEQL VVGHNVSFDR AHIREQYLIQ GSRMRFLDTM SMHMAISGLS SFQRSLWIAA KQGKHKVQPP TKQGQKSQRK ARR GPAISS WDWLDISSVN SLAEVHRLYV GGPPLEKEPR ELFVKGTMKD IRENFQDLMQ YCAQDVWATH EVFQQQLPLF LERC PHPVT LAGMLEMGVS YLPVNQNWER YLAEAQGTYE ELQREMKKSL MDLANDACQL LSGERYKEDP WLWDLEWDLQ EFKQK KAKK VKKEPATASK LPIEGAGAPG DPMDQEDLGP CSEEEEFQQD VMARACLQKL KGTTELLPKR PQHLPGHPGW YRKLCP RLD DPAWTPGPSL LSLQMRVTPK LMALTWDGFP LHYSERHGWG YLVPGRRDNL AKLPTGTTLE SAGVVCPYRA IESLYRK HC LEQGKQQLMP QEAGLAEEFL LTDNSAIWQT VEELDYLEVE AEAKMENLRA AVPGQPLALT ARGGPKDTQP SYHHGNGP Y NDVDIPGCWF FKLPHKDGNS CNVGSPFAKD FLPKMEDGTL QAGPGGASGP RALEINKMIS FWRNAHKRIS SQMVVWLPR SALPRAVIRH PDYDEEGLYG AILPQVVTAG TITRRAVEPT WLTASNARPD RVGSELKAMV QAPPGYTLVG ADVDSQELWI AAVLGDAHF AGMHGCTAFG WMTLQGRKSR GTDLHSKTAT TVGISREHAK IFNYGRIYGA GQPFAERLLM QFNHRLTQQE A AEKAQQMY AATKGLRWYR LSDEGEWLVR ELNLPVDRTE GGWISLQDLR KVQRETARKS QWKKWEVVAE RAWKGGTESE MF NKLESIA TSDIPRTPVL GCCISRALEP SAVQEEFMTS RVNWVVQSSA VDYLHLMLVA MKWLFEEFAI DGRFCISIHD EVR YLVREE DRYRAALALQ ITNLLTRCMF AYKLGLNDLP QSVAFFSAVD IDRCLRKEVT MDCKTPSNPT GMERRYGIPQ GEAL DIYQI IELTKGSLEK RSQPGP

UniProtKB: DNA polymerase subunit gamma-1

-
Macromolecule #2: DNA polymerase subunit gamma-2

MacromoleculeName: DNA polymerase subunit gamma-2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 50.778648 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWLSGYAGPA DGTQQPDAPE HAVAREALVD LCRRRHFFSG TPQQLSTAAL LSGCHARFGP LGVELRKNLA SQWWSSMVVF REQVFAVDS LHQEPGSSQP RDSAFRLVSP ESIREILQDR EPSKEQLVAF LENLLKTSGK LRATLLHGAL EHYVNCLDLV N RKLPFGLA ...String:
MWLSGYAGPA DGTQQPDAPE HAVAREALVD LCRRRHFFSG TPQQLSTAAL LSGCHARFGP LGVELRKNLA SQWWSSMVVF REQVFAVDS LHQEPGSSQP RDSAFRLVSP ESIREILQDR EPSKEQLVAF LENLLKTSGK LRATLLHGAL EHYVNCLDLV N RKLPFGLA QIGVCFHPVS NSNQTPSSVT RVGEKTEASL VWFTPTRTSS QWLDFWLRHR LLWWRKFAMS PSNFSSADCQ DE LGRKGSK LYYSFPWGKE PIETLWNLGD QELLHTYPGN VSTIQGRDGR KNVVPCVLSV SGDVDLGTLA YLYDSFQLAE NSF ARKKSL QRKVLKLHPC LAPIKVALDV GKGPTVELRQ VCQGLLNELL ENGISVWPGY SETVHSSLEQ LHSKYDEMSV LFSV LVTET TLENGLIQLR SRDTTMKEMM HISKLRDFLV KYLASASNVH HHHHH

UniProtKB: DNA polymerase subunit gamma-2

-
Macromolecule #3: DNA (primer strand)

MacromoleculeName: DNA (primer strand) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 7.780008 KDa
SequenceString:
(DG)(DC)(DA)(DT)(DG)(DC)(DG)(DG)(DT)(DC) (DG)(DA)(DG)(DT)(DC)(DT)(DA)(DG)(DA)(DG) (DG)(DA)(DG)(DC)(DT)

-
Macromolecule #4: DNA (template strand)

MacromoleculeName: DNA (template strand) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.162783 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DA)(DT)(DC)(DC)(DG)(DG)(DG)(DC)(DT)(DC) (DC)(DT)(DC)(DT)(DA)(DG)(DA)(DC)(DT) (DC)(DG)(DA)(DC)(DC)(DG)(DC)(DA)(DT)(DG) (DC)

-
Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #6: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: DCP
Molecular weightTheoretical: 467.157 Da
Chemical component information

ChemComp-DCP:
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: CryoSPARC ab-initio model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 516159
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