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- EMDB-39634: The structure of ASFV DNA polymerase in replicating state -

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Basic information

Entry
Database: EMDB / ID: EMD-39634
TitleThe structure of ASFV DNA polymerase in replicating state
Map data
Sample
  • Complex: The ASFV DNA polymerase in replicating state
    • Protein or peptide: DNA polymerase
    • DNA: The primer strand
    • DNA: The template strand
  • Ligand: MAGNESIUM ION
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
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 polymerase family B signature. / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / 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 polymerase family B signature. / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / 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: 2.7 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_39634.png

Downloads & links

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Map

FileDownload / File: emd_39634.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 360 pix.
= 248.4 Å		0.69 Å/pix.
x 360 pix.
= 248.4 Å		0.69 Å/pix.
x 360 pix.
= 248.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0022306016 - 1.7325933
Average (Standard dev.)0.0014253862 (±0.028366445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 248.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39634_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39634_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The ASFV DNA polymerase in replicating state

EntireName: The ASFV DNA polymerase in replicating state
Components
  • Complex: The ASFV DNA polymerase in replicating state
    • Protein or peptide: DNA polymerase
    • DNA: The primer strand
    • DNA: The template strand
  • Ligand: MAGNESIUM ION
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE

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Supramolecule #1: The ASFV DNA polymerase in replicating state

SupramoleculeName: The ASFV DNA polymerase in replicating state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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 primer strand

MacromoleculeName: The primer strand / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 7.681985 KDa
SequenceString:
(DA)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DC)(DC) (DA)(DT)(DG)(DA)(DT)(DT)(DA)(DC)(DG)(DA) (DA)(DT)(DT)(DG)(DC)

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Macromolecule #3: The template strand

MacromoleculeName: The template strand / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 11.677539 KDa
SequenceString:
(DC)(DT)(DG)(DC)(DA)(DC)(DG)(DA)(DA)(DT) (DT)(DA)(DA)(DG)(DC)(DA)(DA)(DT)(DT)(DC) (DG)(DT)(DA)(DA)(DT)(DC)(DA)(DT)(DG) (DG)(DT)(DC)(DA)(DT)(DA)(DG)(DC)(DT)

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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: THYMIDINE-5'-TRIPHOSPHATE

MacromoleculeName: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: TTP
Molecular weightTheoretical: 482.168 Da
Chemical component information

ChemComp-TTP:
THYMIDINE-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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.0 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 290488
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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