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- EMDB-53391: apPol-DNA-nucleotide complex (ternary 3) -

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Basic information

Entry
Database: EMDB / ID: EMD-53391
TitleapPol-DNA-nucleotide complex (ternary 3)
Map dataDeepEMhancer sharpened map
Sample
  • Complex: Ternary complex of apicoplast DNA polymerase, DNA and dGTP with Ca2+
    • Protein or peptide: Plastid replication-repair enzyme
    • DNA: DNA primer strand
    • DNA: DNA template strand
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: CALCIUM ION
KeywordsDNA polymerase / REPLICATION
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / single-stranded DNA binding / 5'-3' DNA helicase activity / DNA-directed DNA polymerase activity / ATP binding
Similarity search - Function
AAA domain / Twinkle-like protein / Archaeal primase DnaG/twinkle-like, TOPRIM domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A ...AAA domain / Twinkle-like protein / Archaeal primase DnaG/twinkle-like, TOPRIM domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / Toprim domain profile. / TOPRIM domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Plastid replication-repair enzyme
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLahiri I / Kumari A
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Other governmentIA/I/20/1/504905
Royal SocietyR179278 United Kingdom
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural basis of multitasking by the apicoplast DNA polymerase from Plasmodium falciparum.
Authors: Anamika Kumari / Theodora Enache / Timothy D Craggs / Janice D Pata / Indrajit Lahiri /
Abstract: Plasmodium falciparum is a eukaryotic pathogen responsible for the majority of malaria-related fatalities. Plasmodium belongs to the phylum Apicomplexa and, like most members of this phylum, contains ...Plasmodium falciparum is a eukaryotic pathogen responsible for the majority of malaria-related fatalities. Plasmodium belongs to the phylum Apicomplexa and, like most members of this phylum, contains a non-photosynthetic plastid called the apicoplast. The apicoplast has its own genome, replicated by a dedicated replisome. Unlike other cellular replisomes, the apicoplast replisome uses a single DNA polymerase (apPol). This suggests that apPol can multitask and catalyse both replicative and lesion bypass synthesis. Replicative synthesis relies on a restrictive active site for high accuracy while lesion bypass typically requires an open active site. This raises the question: how does apPol combine the structural features of multiple DNA polymerases in a single protein? Using single-particle electron cryomicroscopy (cryoEM), we have solved the structures of apPol bound to its undamaged DNA and nucleotide substrates in five pre-chemistry conformational states. We found that apPol can accommodate a nascent base pair with the fingers in an open configuration, which might facilitate the lesion bypass activity. In the fingers-open state, we identified a nascent base pair checkpoint that preferentially selects Watson-Crick base pairs, an essential requirement for replicative synthesis. Taken together, these structural features might explain how apPol balances replicative and lesion bypass synthesis.
History
DepositionApr 11, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53391.png

Downloads & links

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Map

FileDownload / File: emd_53391.map.gz / Format: CCP4 / Size: 45.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 228 pix.
= 241.68 Å		1.06 Å/pix.
x 228 pix.
= 241.68 Å		1.06 Å/pix.
x 228 pix.
= 241.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.0016963042 - 2.042485
Average (Standard dev.)0.0010476987 (±0.024111142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions228228228
Spacing228228228
CellA=B=C: 241.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53391_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: B factor sharpened map

Fileemd_53391_additional_1.map
AnnotationB factor sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53391_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53391_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of apicoplast DNA polymerase, DNA and dGTP with Ca2+

EntireName: Ternary complex of apicoplast DNA polymerase, DNA and dGTP with Ca2+
Components
  • Complex: Ternary complex of apicoplast DNA polymerase, DNA and dGTP with Ca2+
    • Protein or peptide: Plastid replication-repair enzyme
    • DNA: DNA primer strand
    • DNA: DNA template strand
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: CALCIUM ION

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Supramolecule #1: Ternary complex of apicoplast DNA polymerase, DNA and dGTP with Ca2+

SupramoleculeName: Ternary complex of apicoplast DNA polymerase, DNA and dGTP with Ca2+
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 95 KDa

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Macromolecule #1: Plastid replication-repair enzyme

MacromoleculeName: Plastid replication-repair enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 76.473484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPENLYFQ GDEITKKYIK DNIINVDDNI IKKKDIFKLK NENNEITECA FEYFESKKKF DDDIESRFFI INDNNYNEN INLIYKDIKY CGLNIQTTGL EVFDENIRLI QIAVENYPVI IYDMFNINKK DILDGLRKVL ENKNIIKIIQ N GKFDAKFL ...String:
MGSSHHHHHH SQDPENLYFQ GDEITKKYIK DNIINVDDNI IKKKDIFKLK NENNEITECA FEYFESKKKF DDDIESRFFI INDNNYNEN INLIYKDIKY CGLNIQTTGL EVFDENIRLI QIAVENYPVI IYDMFNINKK DILDGLRKVL ENKNIIKIIQ N GKFDAKFL LHNNFKIENI FDTYIASKLL DKNKNMYGFK LNNIVEKYLN VILDKQQQNS VWNNSLLNNN QLFYAARDSS CL LKLYKKL KEEIKKENLH IVNDIENKCI LPICDMELNG IKVDLENLQK STNEILNELN IEKDNLKKKL KDENINVNSQ QQV LKALQK NNVRDISNKL IENTSDSNLK NFLNHEEIIS LRNYRRLYKL YSAFYLKLPL HINTKTNKIH TTFNQLKTFS GRFS SEKPN LQQIPRQKNI REIFIPNDNN IFIIADFKQI ELKIAAEITN DEIMLKAYNN NIDLHTLTAS IITKKNIPDI NKEDR HIAK AINFGLIYGM NYVNLKNYAN TYYGLNMSLD QCLYFYNSFF EHYKGIYKWH NQVKQKRALQ YSTLSNRKVI FPYFSF TKA LNYPVQGTCA DILKLALVDL YDNLKDINGK IILCVHDEII IEVNKKFQEE ALKILVQSME NSASYFLKKV KCEVSVK IA ENWGSKD

UniProtKB: Plastid replication-repair enzyme

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Macromolecule #2: DNA primer strand

MacromoleculeName: DNA primer strand / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 7.714971 KDa
SequenceString:
(DC)(DA)(DG)(DG)(DT)(DG)(DT)(DC)(DA)(DG) (DT)(DC)(DA)(DG)(DC)(DT)(DA)(DG)(DT)(DG) (DC)(DT)(DG)(DA)(DC)

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Macromolecule #3: DNA template strand

MacromoleculeName: DNA template strand / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 11.02308 KDa
SequenceString:
(DG)(DC)(DT)(DA)(DC)(DC)(DG)(DT)(DA)(DG) (DC)(DG)(DT)(DC)(DA)(DG)(DC)(DA)(DC)(DT) (DA)(DG)(DC)(DT)(DG)(DA)(DC)(DT)(DG) (DA)(DC)(DA)(DC)(DC)(DT)(DG)

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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

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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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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

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.0 K / Max: 77.0 K
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 11944 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.8000000000000003 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1993221
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 92787
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5dkt


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9qv9:
apPol-DNA-nucleotide complex (ternary 3)

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