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- EMDB-60926: Structure of Full-Length AsfvPrimPol with polyT DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-60926
TitleStructure of Full-Length AsfvPrimPol with polyT DNA
Map data
Sample
  • Complex: African swine fever virus
    • Protein or peptide: Putative primase C962R
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsPrimase/helicase/DNA-binding / DNA BINDING PROTEIN
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides / helicase activity / DNA replication
Similarity search - Function
Primase, C-terminal 2 / : / Primase C terminal 2 (PriCT-2) / C962R protein N-terminal AEP domain / : / Bacteriophage/plasmid primase, P4, C-terminal / D5 N terminal like / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Putative primase C962R
Similarity search - Component
Biological speciesAfrican swine fever virus / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsXu KE / Chen YT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of Full-Length AsfvPrimPol with polyT DNA
Authors: Xu KE / Chen YT
History
DepositionJul 23, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60926.png

Downloads & links

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Map

FileDownload / File: emd_60926.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.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00732
Minimum - Maximum-0.038187627 - 0.07798031
Average (Standard dev.)0.0004227029 (±0.0034218791)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60926_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_60926_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 : African swine fever virus

EntireName: African swine fever virus
Components
  • Complex: African swine fever virus
    • Protein or peptide: Putative primase C962R
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: African swine fever virus

SupramoleculeName: African swine fever virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: African swine fever virus

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Macromolecule #1: Putative primase C962R

MacromoleculeName: Putative primase C962R / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 111.482273 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MREESWEDHD TIQLTAQRKY LAEVQALETL LTRELSVFLT EPGSKKTNII NRITGKTYAL PSTELLRLYE HLEQCRKQGA LMYFLERQG TYSGLMLDYD LKLNTNAVPP LEPPALSRLC HRIFVHIKNS SVLPEGSHKI HFFFTLKPEV VQGKYGFHVL I PGLKLAAS ...String:
MREESWEDHD TIQLTAQRKY LAEVQALETL LTRELSVFLT EPGSKKTNII NRITGKTYAL PSTELLRLYE HLEQCRKQGA LMYFLERQG TYSGLMLDYD LKLNTNAVPP LEPPALSRLC HRIFVHIKNS SVLPEGSHKI HFFFTLKPEV VQGKYGFHVL I PGLKLAAS TKKSIIGSLQ HDATVQKILH EQGVTNPESC LDPHSASVPS LLYGSSKLNH KPYQLKTGFE LVFDSSDPDY IP IHQIKNL ESYNLVSELS LTNEQGSLVR PVYCAADIAA EKEEEIPTED HSLSILMLHD PEARYLHKIL NLLPPEYYVE YPL WSNVVF ALANTSANYR PLAEWFSQKC PEKWNTGGKE KLEKLWNDAS HHTEKKITKR SIMYWAHKHA PQQYKEIVEQ GYFS ILAEY VYSYNGMLEH YMIAKVIYAM MGNKFVVDVD SNGKYVWFEF VLPGQPMNQG EIWKWRKEVN PDELHIYISE NFSRV MDRI TEHIKYHLSQ PHESNILNYY KKLLKAFERS KSKIFNDSFK KGVIRQAEFL FRQRSFIQTL DTNPHLLGVG NGVLSI ETI PAKLINHFHE HPIHQYTHIC YVPFNPENPW TKLLLNALQD IIPELDARLW IMFYLSTAIF RGLKEALMLL WLGGGCN GK TFLMRLVAMV LGDHYASKLN ISLLTSCRET AEKPNSAFMR LKGRGYGYFE ETNKSEVLNT SRLKEMVNPG DVTARELN Q KQESFQMTAT MVAASNYNFI IDTTDHGTWR RLRHYRSKVK FCHNPDPSNP YEKKEDPRFI HEYIMDPDCQ NAFFSILVY FWEKLQKEYN GQIKKVFCPT IESETEAYRK SQDTLHRFIT ERVVESPSAE TVYNLSEVVT AYAEWYNTNI NVKRHIALEL SQELENSVL EKYLQWSPNK TRILKGCRIL HKFETLQPGE SYIGVSTAGT LLNTPICEPK NKWWEWSPNP SAPPEKEASA P TP

UniProtKB: Putative primase C962R

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

MacromoleculeName: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*T)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.388585 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 6 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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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 TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 1.2 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 253584
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: RANDOM ASSIGNMENT

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