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- EMDB-37530: MPOX E5 hexamer ADP and ssDNA bound and clear primase domain conf... -

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Basic information

Entry
Database: EMDB / ID: EMD-37530
TitleMPOX E5 hexamer ADP and ssDNA bound and clear primase domain conformation
Map data
Sample
  • Complex: MPOX helicase
    • Protein or peptide: Uncoating factor OPG117
    • DNA: DNA (5'-D(P*CP*CP*C)-3')
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
KeywordsMonkey pox / helicase / DNA replication / Complex / VIRAL PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homologyDNA 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. / hydrolase activity / P-loop containing nucleoside triphosphate hydrolase / Uncoating factor OPG117
Function and homology information
Biological speciesMonkeypox virus / Spodoptera frugiperda (fall armyworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsZhang Z / Dong C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371303 China
CitationJournal: Sci Adv / Year: 2024
Title: Essential and multifunctional mpox virus E5 helicase-primase in double and single hexamer.
Authors: Yunxia Xu / Yaqi Wu / Yuanyuan Zhang / Kaiting Gao / Xiaoying Wu / Yaxue Yang / Danyang Li / Biao Yang / Zhengyu Zhang / Changjiang Dong /
Abstract: An outbreak of mpox virus in May 2022 has spread over 110 nonpandemic regions in the world, posing a great threat to global health. Mpox virus E5, a helicase-primase, plays an essential role in DNA ...An outbreak of mpox virus in May 2022 has spread over 110 nonpandemic regions in the world, posing a great threat to global health. Mpox virus E5, a helicase-primase, plays an essential role in DNA replication, but the molecular mechanisms are elusive. Here, we report seven structures of mpox virus E5 in a double hexamer (DH) and six in single hexamer in different conformations, indicating a rotation mechanism for helicase and a coupling action for primase. The DH is formed through the interface of zinc-binding domains, and the central channel density indicates potential double-stranded DNA (dsDNA), which helps to identify dsDNA binding residues Arg, Lys, Lys, and Lys. Our work is important not only for understanding poxviral DNA replication but also for the development of novel therapeutics for serious poxviral infections including smallpox virus and mpox virus.
History
DepositionSep 22, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37530.png

Downloads & links

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Map

FileDownload / File: emd_37530.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.5942995 - 1.050832
Average (Standard dev.)0.0002294938 (±0.018709535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37530_msk_1.map
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AxesZYX

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Half map: #2

Fileemd_37530_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_37530_half_map_2.map
Projections & Slices
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Sample components

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Entire : MPOX helicase

EntireName: MPOX helicase
Components
  • Complex: MPOX helicase
    • Protein or peptide: Uncoating factor OPG117
    • DNA: DNA (5'-D(P*CP*CP*C)-3')
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: MPOX helicase

SupramoleculeName: MPOX helicase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: MPOX helicase apo form
Source (natural)Organism: Monkeypox virus

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Macromolecule #1: Uncoating factor OPG117

MacromoleculeName: Uncoating factor OPG117 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / 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: DNA (5'-D(P*CP*CP*C)-3')

MacromoleculeName: DNA (5'-D(P*CP*CP*C)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 822.588 Da
SequenceString:
(DC)(DC)(DC)

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE
Detailsquantifoil 1.2/1.3 Cu

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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: 2.5 µm / Nominal defocus min: 1.2 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: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107462
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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