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- EMDB-62516: Cryo-EM structure of MPXV core protease in complex with aloxistat... -

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Basic information

Entry
Database: EMDB / ID: EMD-62516
TitleCryo-EM structure of MPXV core protease in complex with aloxistatin(E64d)
Map data
Sample
  • Complex: PROTEASE DIMER
    • Protein or peptide: Core protease I7
  • Ligand: ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate
KeywordsORTHOPOXVIRUSES / MONKEYPOX / PROTEASE / VIRAL REPLICATION / DRUG DISCOVERY / INHIBITOR / E64D / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsLan W / You T / Li D / Dong X / Wang H / Xu J / Wang W / Gao Y / Yang H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81902063 China
CitationJournal: To Be Published
Title: Structure Of Monkeypox I7 Protease In The Apo-Form
Authors: Lan W / You T / Li D / Dong X / Wang H / Xu J / Wang W / Gao Y / Yang H
History
DepositionNov 27, 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_62516.png

Downloads & links

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Map

FileDownload / File: emd_62516.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: 0.2
Minimum - Maximum-4.4799943 - 5.999367
Average (Standard dev.)-0.0015067402 (±0.10118713)
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_62516_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_62516_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
  • Ligand: ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate

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Supramolecule #1: PROTEASE DIMER

SupramoleculeName: PROTEASE DIMER / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: MONKEYPOX I7 PORTEASE IS A DIMER
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: ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1...

MacromoleculeName: ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate
type: ligand / ID: 2 / Number of copies: 2 / Formula: E6D
Molecular weightTheoretical: 344.446 Da
Chemical component information

ChemComp-E6D:
ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate

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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 #1

Image processing ID1
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 424012
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Image processing #2

Image processing ID2
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 424012
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 162.1
Output model

PDB-9kqv:
Cryo-EM structure of MPXV core protease in complex with aloxistatin(E64d)

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