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- EMDB-45407: Ternary structure of Plasmodium falciparum apicoplast DNA polymer... -

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Basic information

Entry
Database: EMDB / ID: EMD-45407
TitleTernary structure of Plasmodium falciparum apicoplast DNA polymerase (exo-minus)
Map data
Sample
  • Complex: Plasmodium falciparum apicoplast DNA polymerase ternary complex
    • Protein or peptide: Plastid replication-repair enzyme
    • DNA: DNA (5'-D(*AP*TP*GP*TP*GP*AP*GP*GP*CP*AP*TP*CP*CP*GP*TP*AP*GP*(2DA))-3')
  • DNA: DNA (5'-D(P*CP*AP*GP*CP*TP*CP*TP*AP*CP*GP*GP*AP*TP*GP*CP*CP*TP*CP*AP*CP*A)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
KeywordsDNA polymerase / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


apicoplast / : / DNA helicase activity / 3'-5' exonuclease activity / single-stranded DNA binding / 5'-3' DNA helicase activity / DNA-directed DNA polymerase / 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) / Homo sapiens (human) / Plasmodium falciparum (isolate 3D7) (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsLo C-Y / Gao Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM142722 United States
CitationJournal: J Mol Biol / Year: 2024
Title: Cryo-EM Structures of the Plasmodium falciparum Apicoplast DNA Polymerase.
Authors: Chen-Yu Lo / Adron R Ung / Tirthankar Koley / Scott W Nelson / Yang Gao /
Abstract: The apicoplast DNA polymerase (apPol) from Plasmodium falciparum is essential for the parasite's survival, making it a prime target for antimalarial therapies. Here, we present cryo-electron ...The apicoplast DNA polymerase (apPol) from Plasmodium falciparum is essential for the parasite's survival, making it a prime target for antimalarial therapies. Here, we present cryo-electron microscopy structures of the apPol in complex with DNA and incoming nucleotide, offering insights into its molecular mechanisms. Our structural analysis reveals that apPol contains critical residues for high-fidelity DNA synthesis, but lacks certain structural elements to confer processive DNA synthesis during replication, suggesting the presence of additional accessory factors. The enzyme exhibits large-scale conformational changes upon DNA and nucleotide binding, particularly within the fingers and thumb subdomains. These movements reveal potential allosteric sites that could serve as targets for drug design. Our findings provide a foundation for advancing the understanding of apPol's unique functional mechanisms and potentially offering new avenues for the development of novel inhibitors and therapeutic interventions against malaria.
History
DepositionJun 18, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45407.png

Downloads & links

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Map

FileDownload / File: emd_45407.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.4965911 - 2.3016438
Average (Standard dev.)0.00015158011 (±0.046413187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.992 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45407_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_45407_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Plasmodium falciparum apicoplast DNA polymerase ternary complex

EntireName: Plasmodium falciparum apicoplast DNA polymerase ternary complex
Components
  • Complex: Plasmodium falciparum apicoplast DNA polymerase ternary complex
    • Protein or peptide: Plastid replication-repair enzyme
    • DNA: DNA (5'-D(*AP*TP*GP*TP*GP*AP*GP*GP*CP*AP*TP*CP*CP*GP*TP*AP*GP*(2DA))-3')
  • DNA: DNA (5'-D(P*CP*AP*GP*CP*TP*CP*TP*AP*CP*GP*GP*AP*TP*GP*CP*CP*TP*CP*AP*CP*A)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Plasmodium falciparum apicoplast DNA polymerase ternary complex

SupramoleculeName: Plasmodium falciparum apicoplast DNA polymerase ternary complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

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Macromolecule #1: DNA (5'-D(P*CP*AP*GP*CP*TP*CP*TP*AP*CP*GP*GP*AP*TP*GP*CP*CP*TP*CP...

MacromoleculeName: DNA (5'-D(P*CP*AP*GP*CP*TP*CP*TP*AP*CP*GP*GP*AP*TP*GP*CP*CP*TP*CP*AP*CP*A)-3')
type: dna / ID: 1 / 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)

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

MacromoleculeName: DNA (5'-D(*AP*TP*GP*TP*GP*AP*GP*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: 6.198027 KDa
SequenceString:
(DT)(DG)(DA)(DT)(DG)(DT)(DG)(DA)(DG)(DG) (DC)(DA)(DT)(DC)(DC)(DG)(DT)(DA)(DG) (2DA)

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Macromolecule #2: Plastid replication-repair enzyme

MacromoleculeName: Plastid replication-repair enzyme / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote)
Molecular weightTheoretical: 74.002891 KDa
SequenceString: DEITKKYIKD NIINVDDNII KKKDIFKLKN ENNEITECAF EYFESKKKFD DDIESRFFII NDNNYNENIN LIYKDIKYCG LNIQTTGLE VFDENIRLIQ IAVENYPVII YDMFNINKKD ILDGLRKVLE NKNIIKIIQN GKFDAKFLLH NNFKIENIFD T YIASKLLD ...String:
DEITKKYIKD NIINVDDNII KKKDIFKLKN ENNEITECAF EYFESKKKFD DDIESRFFII NDNNYNENIN LIYKDIKYCG LNIQTTGLE VFDENIRLIQ IAVENYPVII YDMFNINKKD ILDGLRKVLE NKNIIKIIQN GKFDAKFLLH NNFKIENIFD T YIASKLLD KNKNMYGFKL NNIVEKYLNV ILDKQQQNSV WNNSLLNNNQ LFYAARDSSC LLKLYKKLKE EIKKENLHIV ND IENKCIL PICDMELNGI KVDLENLQKS TNEILNELNI EKDNLKKKLK DENINVNSQQ QVLKALQKNN VRDISNKLIE NTS DSNLKN FLNHEEIISL RNYRRLYKLY SAFYLKLPLH INTKTNKIHT TFNQLKTFSG RFSSEKPNLQ QIPRQKNIRE IFIP NDNNI FIIADFKQIE LKIAAEITND EIMLKAYNNN IDLHTLTASI ITKKNIPDIN KEDRHIAKAI NFGLIYGMNY VNLKN YANT YYGLNMSLDQ CLYFYNSFFE HYKGIYKWHN QVKQKRALQY STLSNRKVIF PYFSFTKALN YPVQGTCADI LKLALV DLY DNLKDINGKI ILCVHDEIII EVNKKFQEEA LKILVQSMEN SASYFLKKVK CEVSVKIAEN WGSKD

UniProtKB: Plastid replication-repair enzyme

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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

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

ChemComp-DGT:
2'-DEOXYGUANOSINE-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: 7.6
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 7.0 sec. / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7000000000000001 µm
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: PDB ENTRY
PDB model - PDB ID:

7sxq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101542
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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