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- PDB-9kqv: Cryo-EM structure of MPXV core protease in complex with aloxistat... -

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Basic information

Entry
Database: PDB / ID: 9kqv
TitleCryo-EM structure of MPXV core protease in complex with aloxistatin(E64d)
ComponentsCore protease I7
KeywordsVIRAL PROTEIN / ORTHOPOXVIRUSES / MONKEYPOX / PROTEASE / VIRAL REPLICATION / DRUG DISCOVERY / INHIBITOR / E64D
Function / homologyPeptidase C57, Vaccinia virus protein I7 / Vaccinia virus I7 processing peptidase / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily / virion component / proteolysis / Chem-E6D / MPXVgp068
Function and homology information
Biological speciesMonkeypox virus
MethodELECTRON MICROSCOPY / single 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, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Core protease I7
B: Core protease I7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8664
Polymers98,1772
Non-polymers6892
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Core protease I7 / I7L / MPXV-COP-062 / MPXV-SL-062 / MPXV-WRAIR062 / MPXVgp068 / Viral core cysteine proteinase / ...I7L / MPXV-COP-062 / MPXV-SL-062 / MPXV-WRAIR062 / MPXVgp068 / Viral core cysteine proteinase / Virion core cysteine protease


Mass: 49088.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus
Gene: I7L, MPXV-CAM1990_02-060, MPXV-COP-062, MPXV-GAB1988_001-061, MPXV-Ikubi-060, MPXV-M2940_FCT-066, MPXV-M2957_Lagos-066, MPXV-M3021_Delta-066, MPXV-M5320_M15_Bayelsa-059, MPXV-Nig_SEV71_2_82- ...Gene: I7L, MPXV-CAM1990_02-060, MPXV-COP-062, MPXV-GAB1988_001-061, MPXV-Ikubi-060, MPXV-M2940_FCT-066, MPXV-M2957_Lagos-066, MPXV-M3021_Delta-066, MPXV-M5320_M15_Bayelsa-059, MPXV-Nig_SEV71_2_82-061, MPXV-PCH-063, MPXV-Singapore-066, MPXV-SL-062, MPXV-UK_P1-066, MPXV-UK_P2-066, MPXV-UK_P3-066, MPXV-UTC-057, MPXV-W_Nigeria-061, MPXV-WRAIR062, MPXV297957_057, MPXV298464_048, MPXV_DRC_Yandongi_069, MPXV_LIB1970_184_073, MPXV_RCG2003_358_073, MPXV_SUD2005_01_069, MPXV_ZAI1979_005_073, MPXVgp068, PDLMKLCO_00071
Production host: Escherichia coli (E. coli)
References: UniProt: Q5IXV7, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-E6D / ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate


Mass: 344.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32N2O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PROTEASE DIMER / Type: COMPLEX / Details: MONKEYPOX I7 PORTEASE IS A DIMER / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Monkeypox virus
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
12.93FSC 0.143 CUT-OFF42401219KQVPOINT
22.93FSC 0.143 CUT-OFF42401219KQVPOINT
32.93FSC 0.143 CUT-OFF42401229KQVPOINT
42.93FSC 0.143 CUT-OFF42401229KQVPOINT
Atomic model buildingB value: 162.1 / Protocol: AB INITIO MODEL / Space: REAL

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