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- EMDB-61294: Cryo-EM structure of MPXV protease in complex with compound A4 -

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Basic information

Entry
Database: EMDB / ID: EMD-61294
TitleCryo-EM structure of MPXV protease in complex with compound A4
Map data
Sample
  • Complex: Protease Dimer
    • Protein or peptide: Core protease I7
    • Protein or peptide: A1ECL-DI8-ALA-AEM
KeywordsOrthopoxviruses / mpox / Protease / Viral replication / Drug discovery / inhibitor / VIRAL PROTEIN
Function / homologyPeptidase C57, Vaccinia virus protein I7 / Vaccinia virus I7 processing peptidase / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily / virion component / proteolysis / MPXVgp068
Function and homology information
Biological speciesMonkeypox virus / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsGao Y / Xie X / Lan W / Wang W / Yang H
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82130105 China
National Natural Science Foundation of China (NSFC)81902063 China
CitationJournal: To Be Published
Title: Cryo-EM structure of MPXV protease in complex with compound A4
Authors: Gao Y / Xie X / Lan W / Wang W / Yang H
History
DepositionAug 25, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61294.png

Downloads & links

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Map

FileDownload / File: emd_61294.map.gz / Format: CCP4 / Size: 83.7 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 280 pix.
= 232.96 Å		0.83 Å/pix.
x 280 pix.
= 232.96 Å		0.83 Å/pix.
x 280 pix.
= 232.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-4.2752347 - 6.535129
Average (Standard dev.)-0.0009133146 (±0.09016592)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 232.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61294_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_61294_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 : Protease Dimer

EntireName: Protease Dimer
Components
  • Complex: Protease Dimer
    • Protein or peptide: Core protease I7
    • Protein or peptide: A1ECL-DI8-ALA-AEM

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Supramolecule #1: Protease Dimer

SupramoleculeName: Protease Dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Protease Dimer in complex with compound A4
Source (natural)Organism: Monkeypox virus

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Macromolecule #1: Core protease I7

MacromoleculeName: Core protease I7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 49.088477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MERYTDLVIS KIPELGFTNL LCHIYSLAGL CSNIDVSKFL TNCNGYVVEK YDKSTTAGKV SCIPIGMMLE LVESGHLSRP NSSDELDQK KELTDELTTR YHSIYDVFEL PTSIPLAYFF KPQLREKVSK AIDFSQMDLK IDDLSRKGIH TGENPKVVKM K IEPERGAW ...String:
MERYTDLVIS KIPELGFTNL LCHIYSLAGL CSNIDVSKFL TNCNGYVVEK YDKSTTAGKV SCIPIGMMLE LVESGHLSRP NSSDELDQK KELTDELTTR YHSIYDVFEL PTSIPLAYFF KPQLREKVSK AIDFSQMDLK IDDLSRKGIH TGENPKVVKM K IEPERGAW MSNRSIKNLV SQFAYGSEVD YIGQFDMRFL NSLAIHEKFD AFMNKHILSY ILKDKIKSST SRFVMFGFCY LS HWKCVIY DKKQCLVSFY DSGGNIPTEF HHYNNFYFYS FSDGFNTNHR HSVLDNTNCD IDVLFRFFEC TFGAKIGCIN VEV NQLLES ECGMFISLFM ILCTRTPPKS FKSLKKVYTF FKFLADKKMT LFKSILFNLQ DLSLYITETD NAGLKEYKRM EKWT KKSIN VICDKLTTKL NRIVDDDE

UniProtKB: MPXVgp068

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Macromolecule #2: A1ECL-DI8-ALA-AEM

MacromoleculeName: A1ECL-DI8-ALA-AEM / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 549.589 Da
SequenceString:
(A1ECL)(DI8)A(AEM)

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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

MicroscopeTFS 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: 1.8 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: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 717581
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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