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- EMDB-52815: Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB... -

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Basic information

Entry
Database: EMDB / ID: EMD-52815
TitleChimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in replication conformer
Map dataMain map
Sample
  • Complex: Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in replication conformer
    • 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


gamma DNA polymerase complex / mitochondrial chromosome / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / DNA polymerase processivity factor activity / mitochondrial nucleoid / 5'-deoxyribose-5-phosphate lyase activity ...gamma DNA polymerase complex / mitochondrial chromosome / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / DNA polymerase processivity factor activity / mitochondrial nucleoid / 5'-deoxyribose-5-phosphate lyase activity / base-excision repair, gap-filling / DNA polymerase binding / Transcriptional activation of mitochondrial biogenesis / DNA-templated DNA replication / protease binding / double-stranded DNA binding / in utero embryonic development / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrial matrix / chromatin binding / mitochondrion / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
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-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: 2.54 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

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Structure visualization

Supplemental images

emd_52815.png

Downloads & links

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Map

FileDownload / File: emd_52815.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)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-25.178535 - 43.069735999999999
Average (Standard dev.)-0.0069426037 (±0.95454246)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_52815_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Unsharpened map

Fileemd_52815_additional_1.map
AnnotationUnsharpened map
Projections & Slices
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Additional map: DeepEMhancer map

Fileemd_52815_additional_2.map
AnnotationDeepEMhancer map
Projections & Slices
AxesZYX

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Half map: Half map A

Fileemd_52815_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_52815_half_map_2.map
AnnotationHalf map B
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Sample components

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Entire : Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB...

EntireName: Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in replication conformer
Components
  • Complex: Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in replication conformer
    • 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

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

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

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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: Mus musculus (house mouse)

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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: Homo sapiens (human)

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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: Mus musculus (house mouse)
Molecular weightTheoretical: 135.078188 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHVSS SVLDPVPSDG RPPSQMPSSE NGQLRLNPLL IQMLSRGLHE QIFGCGGEMP DEAAVQRSVE HLQKHGLWGQ PATPLPDVE LRLPRLFGGN LDQHFRLLAQ KQSLPYLEAA ASLLEAQLPP EPKSWAWAEG WTRYGPEGEA EPVAIPEERA L VFDVEVCL ...String:
MHHHHHHVSS SVLDPVPSDG RPPSQMPSSE NGQLRLNPLL IQMLSRGLHE QIFGCGGEMP DEAAVQRSVE HLQKHGLWGQ PATPLPDVE LRLPRLFGGN LDQHFRLLAQ KQSLPYLEAA ASLLEAQLPP EPKSWAWAEG WTRYGPEGEA EPVAIPEERA L VFDVEVCL AEGTCPTLAV AISPSAWYSW CSRRLVEERY SWTSQLSPAD LIPLGGSTSA SSSTKQDGQE QLVVGHNVSF DR AHIREQY LIQDSRMRFL DTMSMHMAIS GLSSFQRSLW MGAKQGKHKT QQSTKRGQKS PRKANGPAIS SWDWMDISSA NNL ADVHNL YVGGPPLEKE PRELFVKGSM RDIRENFQDL MQYCARDVWA TFEVFQQQLP LFLERCPHPV TLAGMLEMGV SYLP VNQNW ERYLTEAQNT YEELQREMKK SLMDLANDAC QLLSGERYKE DPWLWDLEWD LQEFKQKKAK KVKKPASASK LPIEG AGPF GDPMDQEDPG PPSEEEELQR SVTAHNRLQQ LRSTTDLLPK RPQHLPGHPG WYRKLCPRLD DPAWAPGPSL LSLQMR VTP KLMALTWDGF PLHYSDSHGW GYLVPGRRDN LTEPPVSPTV ESAAVTCPYR AIESLYRKHC LEQGKQQLEP QEVDLAE EF LLTDSSAMWQ TVEELGCLDV EAEAKMENSG LSQPLVLPAA CAPKSSQPTY HHGNGPYNDV NIPGCWFFKL PHKDGNNY N VGSPFAKDFL PKMEDGTLQA GPGGASGPRA LEINKMISFW RNAHKRISSQ MVVWLPRSAL PRVVTRHPSF DEEGHYGAI LPQVVTAGTI TRRAVEPTWL TASNARPDRV GSELKAMVQA PPGYVLVGAD VDSQELWIAA VLGDAHFAGM HGCTAFGWMT LQGRKSRGT DLHSKTAATV GISREHAKIF NYGRIYGAGQ SFAERLLMQF NHRLTRQEAA EKAQQMYAVT KGLRRYRLSA D GEWLVKQL NLPVDRTEDG WVSLQDLRMI RREASRKSRW KKWEVASERA WTGGTESEMF NKLESIAMSD TPRTPVLGCC IS RALEPSV VQGEFITSRV NWVVQSSAVD YLHLMLVAMK WLFEEFAIDG RFCISIHDEV RYLVREEDRY RAALALQITN LLT RCMFAY KLGLNDLPQS VAFFSAVDID QCLRKEVTMD CKTPSNPTGM ERRYGIPQGE ALDIYQIIEL TKGSLEKRSQ PGP

UniProtKB: DNA polymerase subunit gamma-1

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Macromolecule #2: DNA polymerase subunit gamma-2

MacromoleculeName: DNA polymerase subunit gamma-2 / type: protein_or_peptide / ID: 2 / Details: A169T (Single Nucleotide Polymorphism) / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.229684 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDAGQPELLT ERSSPKGGHV KSHAELEGNG EHPEAPGSGE GSEALLEICQ RRHFLSGSKQ QLSRDSLLSG CHPGFGPLGV ELRKNLAAE WWTSVVVFRE QVFPVDALHH KPGPLLPGDS AFRLVSAETL REILQDKELS KEQLVTFLEN VLKTSGKLRE N LLHGALEH ...String:
MDAGQPELLT ERSSPKGGHV KSHAELEGNG EHPEAPGSGE GSEALLEICQ RRHFLSGSKQ QLSRDSLLSG CHPGFGPLGV ELRKNLAAE WWTSVVVFRE QVFPVDALHH KPGPLLPGDS AFRLVSAETL REILQDKELS KEQLVTFLEN VLKTSGKLRE N LLHGALEH YVNCLDLVNK RLPYGLAQIG VCFHPVFDTK QIRNGVKSIG EKTEASLVWF TPPRTSNQWL DFWLRHRLQW WR KFAMSPS NFSSSDCQDE EGRKGNKLYY NFPWGKELIE TLWNLGDHEL LHMYPGNVSK LHGRDGRKNV VPCVLSVNGD LDR GMLAYL YDSFQLTENS FTRKKNLHRK VLKLHPCLAP IKVALDVGRG PTLELRQVCQ GLFNELLENG ISVWPGYLET MQSS LEQLY SKYDEMSILF TVLVTETTLE NGLIHLRSRD TTMKEMMHIS KLKDFLIKYI SSAKNVHHHH HH

UniProtKB: DNA polymerase subunit gamma-2

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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)

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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)

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

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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

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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: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 713960
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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