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- EMDB-62891: Cryo-EM structure of ASFV DNA polymerase in a DNA replication state -

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Basic information

Entry
Database: EMDB / ID: EMD-62891
TitleCryo-EM structure of ASFV DNA polymerase in a DNA replication state
Map data
Sample
  • Complex: ASFV DNA polymerase with dsDNA
    • Protein or peptide: DNA polymerase
    • DNA: DNA (5'-D(P*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3')
    • DNA: DNA (5'-D(P*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*A)-3')
  • Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsVirus / DNA polymerase / ASFV / DNA BINDING PROTEIN/DNA / DNA BINDING 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 speciesAsfarviridae (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsHu Z / Yan R
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of ASFV DNA polymerase in a DNA replication state
Authors: Hu Z / Yan R
History
DepositionDec 28, 2024-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62891.png

Downloads & links

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Map

FileDownload / File: emd_62891.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.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-3.8321242 - 6.332411
Average (Standard dev.)-0.0005521392 (±0.11259163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62891_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_62891_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 : ASFV DNA polymerase with dsDNA

EntireName: ASFV DNA polymerase with dsDNA
Components
  • Complex: ASFV DNA polymerase with dsDNA
    • Protein or peptide: DNA polymerase
    • DNA: DNA (5'-D(P*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3')
    • DNA: DNA (5'-D(P*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*A)-3')
  • Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ASFV DNA polymerase with dsDNA

SupramoleculeName: ASFV DNA polymerase with dsDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Asfarviridae (virus)

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Macromolecule #1: DNA polymerase

MacromoleculeName: DNA polymerase / type: protein_or_peptide / ID: 1
Details: Sequence reference for strain 'Asfarviridae' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A7D5JBM0.
Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Asfarviridae (virus)
Molecular weightTheoretical: 115.127031 KDa
Recombinant expressionOrganism: Eukaryota (eukaryotes)
SequenceString: ISIMDRSEIV ARENPVITQR VTNLLQTNAP LLFMPIDIHE VRYGAYTLFM YGSLENGYKA EVRIENIPVF FDVQIEFNDT NQLFLKSLL TAENIVYERL ETLTQRPVMG YREKEKEFAP YIRIFFKSLY ERRKAITYLN NMGYNTAADD TTCYYRMVSR E LKLPLTSW ...String:
ISIMDRSEIV ARENPVITQR VTNLLQTNAP LLFMPIDIHE VRYGAYTLFM YGSLENGYKA EVRIENIPVF FDVQIEFNDT NQLFLKSLL TAENIVYERL ETLTQRPVMG YREKEKEFAP YIRIFFKSLY ERRKAITYLN NMGYNTAADD TTCYYRMVSR E LKLPLTSW IQLQHYSYEP RGLVHRFSVT PEDLVSYQND GPTDHSIVMA YDIETYSPVK GTVPDPNQAN DVVFMICMRI FW IHSTEPL ASTCITMAPC KKSSEWTTIL CSSEKNLLLS FAEQFSRWAP DICTGFNDSR YDWPFIVEKS MQHGILEEIF NKM SLFWHQ KLDTILKCYY VKEKRVKISA EKSIISSFLH TPGCLPIDVR NMCMQLYPKA EKTSLKAFLE NCGLDSKVDL PYHL MWKYY ETRDSEKIAD VAYYCIIDAQ RCQDLLVRHN VIPDRREVGI LSYTSLYDCI YYAGGHKVCN MLIAYAIHDE YGRIA CSTI ARGKREHGKY PGAFVIDPVK GLEQDKPTTG LDFASLYPSL IMAYNFSPEK FVASRDEANS LMAKGESLHY VSFHFN NRL VEGWFVWHNN VPDKMGLYPK VLIDLLNKRT ALKQELKKLG EKKECIHESH PGFKELQFRH AMVDAKQKAL KIFMNTF YG EAGNNLSPFF LLPLAGGVTS SGQYNLKLVY NFVINKGYGI KYGDTDSLYI TCPDSLYTEV TDAYLNSQKT IKHYEQLC H EKVLLSMKAM STLCAEVNEY LRQDNGTSYL RMAYEEVLFP VCFTGKKKYY GIAHVNTPNF NTKELFIRGI DIIKQGQTK LTKTIGTRIM EESMKLRRPE DHRPPLIEIV KTVLKDAVVN MKQWNFEDFI QTDAWRPDKD NKAVQIFMSR MHARREQLKK HGAAASQFA EPEPGERFSY VIVEKQVQFD IQGHRTDSSR KGDKMEYVSE AKAKNLPIDI LFYINNYVLG LCARFINENE E FQPPDNVS NKDEYAQRRA KSYLQKFVQS IHPK

UniProtKB: DNA polymerase

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Macromolecule #2: DNA (5'-D(P*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3')

MacromoleculeName: DNA (5'-D(P*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Asfarviridae (virus)
Molecular weightTheoretical: 5.067301 KDa
SequenceString:
(DT)(DA)(DA)(DG)(DG)(DT)(DA)(DG)(DG)(DG) (DG)(DA)(DG)(DG)(DA)(DT)

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Macromolecule #3: DNA (5'-D(P*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*A)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Asfarviridae (virus)
Molecular weightTheoretical: 3.229125 KDa
SequenceString:
(DA)(DT)(DC)(DC)(DT)(DC)(DC)(DC)(DC)(DT) (DA)

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Macromolecule #4: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: DCP
Molecular weightTheoretical: 467.157 Da
Chemical component information

ChemComp-DCP:
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 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: NITROGEN

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 1.8 µm / Calibrated defocus min: 1.4000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 696619
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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