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- EMDB-39638: The structure of ASFV DNA polymerase in editing state -

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Basic information

Entry
Database: EMDB / ID: EMD-39638
TitleThe structure of ASFV DNA polymerase in editing state
Map dataMaybe processed by DeepEMhancer
Sample
  • Complex: The ASFV DNA polymerase in editing state
    • Protein or peptide: DNA polymerase
    • DNA: The template strand
    • DNA: The primer strand
KeywordsDNA polymerase / VIRAL PROTEIN/DNA / VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


viral DNA genome replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding / DNA binding
Similarity search - Function
: / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family ...: / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKuai L / Sun JQ / Peng Q / Shi Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81871658 China
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Cryo-EM structure of DNA polymerase of African swine fever virus.
Authors: Lu Kuai / Junqing Sun / Qi Peng / Xuejin Zhao / Bin Yuan / Sheng Liu / Yuhai Bi / Yi Shi /
Abstract: African swine fever virus (ASFV) is one of the most important causative agents of animal diseases and can cause highly fatal diseases in swine. ASFV DNA polymerase (DNAPol) is responsible for genome ...African swine fever virus (ASFV) is one of the most important causative agents of animal diseases and can cause highly fatal diseases in swine. ASFV DNA polymerase (DNAPol) is responsible for genome replication and highly conserved in all viral genotypes showing an ideal target for drug development. Here, we systematically determined the structures of ASFV DNAPol in apo, replicating and editing states. Structural analysis revealed that ASFV DNAPol had a classical right-handed structure and showed the highest similarity to the structure of human polymerase delta. Intriguingly, ASFV DNAPol has a much longer fingers subdomain, and the thumb and palm subdomain form a unique interaction that has never been seen. Mutagenesis work revealed that the loss of this unique interaction decreased the enzymatic activity. We also found that the β-hairpin of ASFV DNAPol is located below the template strand in the editing state, which is different from the editing structures of other known B family DNAPols with the β-hairpin above the template strand. It suggests that B family DNAPols have evolved two ways to facilitate the dsDNA unwinding during the transition from replicating into editing state. These findings figured out the working mechanism of ASFV DNAPol and will provide a critical structural basis for the development of antiviral drugs.
History
DepositionMar 31, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39638.png

Downloads & links

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Map

FileDownload / File: emd_39638.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMaybe processed by DeepEMhancer
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.0016957937 - 1.8164539
Average (Standard dev.)0.0023783394 (±0.037344977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39638_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39638_half_map_2.map
Projections & Slices
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Sample components

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Entire : The ASFV DNA polymerase in editing state

EntireName: The ASFV DNA polymerase in editing state
Components
  • Complex: The ASFV DNA polymerase in editing state
    • Protein or peptide: DNA polymerase
    • DNA: The template strand
    • DNA: The primer strand

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Supramolecule #1: The ASFV DNA polymerase in editing state

SupramoleculeName: The ASFV DNA polymerase in editing state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: African swine fever virus

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Macromolecule #1: DNA polymerase

MacromoleculeName: DNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 139.719047 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MISIMDRSEI VARENPVITQ RVTNLLQTNA PLLFMPIDIH EVRYGAYTLF MYGSLENGYK AEVRIENIPV FFDVQIEFND TNQLFLKSL LTAENIVYER LETLTQRPVM GYREKEKEFA PYIRIFFKSL YERRKAITYL NNMGYNTAAD DTTCYYRMVS R ELKLPLTS ...String:
MISIMDRSEI VARENPVITQ RVTNLLQTNA PLLFMPIDIH EVRYGAYTLF MYGSLENGYK AEVRIENIPV FFDVQIEFND TNQLFLKSL LTAENIVYER LETLTQRPVM GYREKEKEFA PYIRIFFKSL YERRKAITYL NNMGYNTAAD DTTCYYRMVS R ELKLPLTS WIQLQHYSYE PRGLVHRFSV TPEDLVSYQN DGPTDHSIVM AYDIETYSPV KGTVPDPNQA NDVVFMICMR IF WIHSTEP LASTCITMAP CKKSSEWTTI LCSSEKNLLL SFAEQFSRWA PDICTGFNDS RYDWPFIVEK SMQHGILEEI FNK MSLFWH QKLDTILKCY YVKEKRVKIS AEKSIISSFL HTPGCLPIDV RNMCMQLYPK AEKTSLKAFL ENCGLDSKVD LPYH LMWKY YETRDSEKIA DVAYYCIIDA QRCQDLLVRH NVIPDRREVG ILSYTSLYDC IYYAGGHKVC NMLIAYAIHD EYGRI ACST IARGKREHGK YPGAFVIDPV KGLEQDKPTT GLDFASLYPS LIMAYNFSPE KFVASRDEAN SLMAKGESLH YVSFHF NNR LVEGWFVRHN NVPDKMGLYP KVLIDLLNKR TALKQELKKL GEKKECIHES HPGFKELQFR HAMVDAKQKA LKIFMNT FY GEAGNNLSPF FLLPLAGGVT SSGQYNLKLV YNFVINKGYG IKYGDTDSLY ITCPDSLYTE VTDAYLNSQK TIKHYEQL C HEKVLLSMKA MSTLCAEVNE YLRQDNGTSY LRMAYEEVLF PVCFTGKKKY YGIAHVNTPN FNTKELFIRG IDIIKQGQT KLTKTIGTRI MEESMKLRRP EDHRPPLIEI VKTVLKDAVV NMKQWNFEDF IQTDAWRPDK DNKAVQIFMS RMHARREQLK KHGAAASQF AEPEPGERFS YVIVEKQVQF DIQGHRTDSS RKGDKMEYVS EAKAKNLPID ILFYINNYVL GLCARFINEN E EFQPPDNV SNKDEYAQRR AKSYLQKFVQ SIHPKDKSVI KQGNVHRQCY KYIHQEIKKK IGIFADLYKE FFNNTTNPIE SF IQSTQFM IQYFDGEQKV NHSMKKMVEQ HATASNRAGK PAGNPAGNAL MRAIFTQLIT EEKKIVQALY NKGDAIHDLL TYI INNINY KIATFQTKQM LTFEFSSTHV ELLLKLNKTW LILAGIHVAK KHLQAFLDSY NNESPSRTFI QQAIEEECGS IKPS CYDFI S

UniProtKB: DNA polymerase

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Macromolecule #2: The template strand

MacromoleculeName: The template strand / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 8.461457 KDa
SequenceString:
(DA)(DA)(DT)(DG)(DG)(DT)(DA)(DG)(DG)(DG) (DG)(DA)(DA)(DG)(DG)(DA)(DT)(DC)(DG)(DT) (DA)(DT)(DG)(DG)(DC)(DC)(DT)

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Macromolecule #3: The primer strand

MacromoleculeName: The primer strand / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 6.921475 KDa
SequenceString:
(DA)(DG)(DG)(DC)(DC)(DA)(DT)(DA)(DC)(DG) (DA)(DT)(DC)(DC)(DT)(DT)(DC)(DC)(DC)(DC) (DT)(DA)(DC)

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 356638
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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