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- EMDB-60678: The Cryo-EM structure of MPXV E5 in complex with ssDNA focused on... -

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Basic information

Entry
Database: EMDB / ID: EMD-60678
TitleThe Cryo-EM structure of MPXV E5 in complex with ssDNA focused on primase and Zn binding domain
Map data
Sample
  • Complex: MPXV E5 in complex with ssDNA focused on primase and Zn binding domain
    • Protein or peptide: Primase D5
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordscomplex / VIRAL PROTEIN
Function / homology
Function and homology information


helicase activity / hydrolase activity
Similarity search - Function
DNA primase/nucleoside triphosphatase, C-terminal / Poxvirus D5 protein-like / : / 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
Uncoating factor OPG117
Similarity search - Component
Biological speciesMonkeypox virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsCheng YX / Han P / Wang H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270157 China
CitationJournal: Nat Commun / Year: 2025
Title: Assembly and breakage of head-to-head double hexamer reveals mpox virus E5-catalyzed DNA unwinding initiation.
Authors: Yingxian Cheng / Pu Han / Qi Peng / Ruili Liu / Hao Liu / Bin Yuan / Yunfei Zhao / Lu Kuai / Jianxun Qi / Kai Miao / Yi Shi / George Fu Gao / Han Wang /
Abstract: The replicative helicase-catalyzed unwinding of the DNA double helix is the initiation of DNA replication. Helicases and primases are functionally related enzymes that have even been expressed as ...The replicative helicase-catalyzed unwinding of the DNA double helix is the initiation of DNA replication. Helicases and primases are functionally related enzymes that have even been expressed as fusion proteins in some organisms and viruses. However, the mechanism underlying DNA unwinding initiation by these helicase-primase fusion enzymes and the functional association between domains have not been elucidated. Herein, we report the cryo-EM structures of mpox virus E5, the founding member of these helicase-primase enzymes, in various enzymatic stages. Notably, E5 forms a head-to-head double hexamer encircling dsDNA, disrupted by the conformational rearrangement of primase domains upon nucleotide incorporation. Five E5-ssDNA-ATP structures further support an ATP cycle-driven non-classical escort model for E5 translocation. Finally, the helicase domain is found to enhance the primase function as a DNA scaffold. Together, our data shed light on the E5-mediated DNA unwinding model including dsDNA loading, DNA melting, ssDNA translocation, and provide a reasonable interpretation for evolutionary preservation of helicase-primase fusion from a functional perspective.
History
DepositionJul 1, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60678.png

Downloads & links

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Map

FileDownload / File: emd_60678.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 500 pix.
= 440. Å		0.88 Å/pix.
x 500 pix.
= 440. Å		0.88 Å/pix.
x 500 pix.
= 440. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.0017239499 - 5.07545
Average (Standard dev.)0.00010871846 (±0.008460145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60678_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_60678_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : MPXV E5 in complex with ssDNA focused on primase and Zn binding domain

EntireName: MPXV E5 in complex with ssDNA focused on primase and Zn binding domain
Components
  • Complex: MPXV E5 in complex with ssDNA focused on primase and Zn binding domain
    • Protein or peptide: Primase D5
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: MPXV E5 in complex with ssDNA focused on primase and Zn binding domain

SupramoleculeName: MPXV E5 in complex with ssDNA focused on primase and Zn binding domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Monkeypox virus

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Macromolecule #1: Primase D5

MacromoleculeName: Primase D5 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 90.476344 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDAAIRGNDV IFVLKTIGVP SACRQNEDPR FVEAFKCDEL ERYIDNNPEC TLFESLRDEE AYSIVRIFMD VDLDACLDEI DYLTAIQDF IIEVSNCVAR FAFTECGAIH ENVIKSMRSN FSLTKSTNRD KTSFHIIFLD TYTTMDTLIA MKRTLLELSR S SENPLTRS ...String:
MDAAIRGNDV IFVLKTIGVP SACRQNEDPR FVEAFKCDEL ERYIDNNPEC TLFESLRDEE AYSIVRIFMD VDLDACLDEI DYLTAIQDF IIEVSNCVAR FAFTECGAIH ENVIKSMRSN FSLTKSTNRD KTSFHIIFLD TYTTMDTLIA MKRTLLELSR S SENPLTRS IDTAVYRRKT TLRVVGTRKN PNCDTIHVMQ PPHDNIEDYL FTYVDMNNNS YYFSLQRRLE DLVPDKLWEP GF ISFEDAI KRVSKIFINS IINFNDLDEN NFTTVPLVID YVTPCALCKK RSHKHPHQLS LENGAIRIYK TGNPHSCKVK IVP LDGNKL FNIAQRILDT NSVLLTERGD HIVWINNSWK FNSEEPLITK LILSIRHQLP KEYSSELLCP RKRKTVEANI RDML VDSVE TDTYPDKLPF KNGVLDLVDG MFYSGDDAKK YTCTVSTGFK FDDTKFVEDS PEMEELMNII NDIQPLTDEN KKNRE LYEK TLSSCLCGAT KGCLTFFFGE TATGKSTTKR LLKSAIGDLF VETGQTILTD VLDKGPNPFI ANMHLKRSVF CSELPD FAC SGSKKIRSDN IKKLTEPCVI GRPCFSNKIN NRNHATIIID TNYKPVFDRI DNALMRRIAV VRFRTHFSQP SGREAAE NN DAYDKVKLLD EGLDGKIQNN RYRFAFLYLL VKWYKKYHIP IMKLYPTPEE IPDFAFYLKI GTLLVSSSVK HIPLMTDL S KKGYILYDNV VTLPLTTFQQ KISKYFNSRL FGHDIESFIN RHKKFANVSD EYLQYIFIED ISSP

UniProtKB: Uncoating factor OPG117

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*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: 7.4
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: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold2 model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 396940
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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