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- EMDB-37882: Structure of ATP-rs-Form AsfvPrimPol Hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-37882
TitleStructure of ATP-rs-Form AsfvPrimPol Hexamer
Map data
Sample
  • Complex: C962R ATP-rs-Form hexamer
    • DNA: DNA (25-MER)
    • DNA: DNA (5'-D(P*AP*AP*AP*A)-3')
    • Protein or peptide: Putative primase C962R
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsVIRAL PROTEIN / DNA BINDING PROTEIN-DNA COMPLEX
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 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsShi TH / Guo YY / Yan RH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of ADP-Form AsfvPrimPol Hexamer
Authors: Shi TH / Guo YY / Yan RH
History
DepositionOct 25, 2023-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37882.png

Downloads & links

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Map

FileDownload / File: emd_37882.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 420.48 Å		1.1 Å/pix.
x 384 pix.
= 420.48 Å		1.1 Å/pix.
x 384 pix.
= 420.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.44131356 - 1.1639992
Average (Standard dev.)-0.002544247 (±0.037520114)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 420.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37882_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_37882_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 : C962R ATP-rs-Form hexamer

EntireName: C962R ATP-rs-Form hexamer
Components
  • Complex: C962R ATP-rs-Form hexamer
    • DNA: DNA (25-MER)
    • DNA: DNA (5'-D(P*AP*AP*AP*A)-3')
    • Protein or peptide: Putative primase C962R
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: C962R ATP-rs-Form hexamer

SupramoleculeName: C962R ATP-rs-Form hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: African swine fever virus

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Macromolecule #1: DNA (25-MER)

MacromoleculeName: DNA (25-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.559863 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)

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Macromolecule #2: DNA (5'-D(P*AP*AP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*AP*AP*A)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.20787 KDa
SequenceString:
(DA)(DA)(DA)(DA)

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Macromolecule #3: Putative primase C962R

MacromoleculeName: Putative primase C962R / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 112.721516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 TPLEDYKD DDDK

UniProtKB: Putative primase C962R

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Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 6 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / 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: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38908
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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