+Open data
-Basic information
Entry | Database: PDB / ID: 8x8q | ||||||
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Title | Structure of enterovirus protease in complex host factor | ||||||
Components |
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Keywords | CELL CYCLE / host protein / VIRAL PROTEIN / CELL INVASION | ||||||
Function / homology | Function and homology information protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / positive regulation of muscle cell differentiation / cysteine-type peptidase activity / viral process ...protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / positive regulation of muscle cell differentiation / cysteine-type peptidase activity / viral process / PKMTs methylate histone lysines / actin binding / RNA polymerase II-specific DNA-binding transcription factor binding / host cell cytoplasm / transcription coactivator activity / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / proteolysis / nucleoplasm / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Enterovirus A71 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å | ||||||
Authors | Gao, X. / Cui, S. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: The EV71 2A protease occupies the central cleft of SETD3 and disrupts SETD3-actin interaction. Authors: Xiaopan Gao / Bei Wang / Kaixiang Zhu / Linyue Wang / Bo Qin / Kun Shang / Wei Ding / Jianwei Wang / Sheng Cui / Abstract: SETD3 is an essential host factor for the replication of a variety of enteroviruses that specifically interacts with viral protease 2A. However, the interaction between SETD3 and the 2A protease has ...SETD3 is an essential host factor for the replication of a variety of enteroviruses that specifically interacts with viral protease 2A. However, the interaction between SETD3 and the 2A protease has not been fully characterized. Here, we use X-ray crystallography and cryo-electron microscopy to determine the structures of SETD3 complexed with the 2A protease of EV71 to 3.5 Å and 3.1 Å resolution, respectively. We find that the 2A protease occupies the V-shaped central cleft of SETD3 through two discrete sites. The relative positions of the two proteins vary in the crystal and cryo-EM structures, showing dynamic binding. A biolayer interferometry assay shows that the EV71 2A protease outcompetes actin for SETD3 binding. We identify key 2A residues involved in SETD3 binding and demonstrate that 2A's ability to bind SETD3 correlates with EV71 production in cells. Coimmunoprecipitation experiments in EV71 infected and 2A expressing cells indicate that 2A interferes with the SETD3-actin complex, and the disruption of this complex reduces enterovirus replication. Together, these results reveal the molecular mechanism underlying the interplay between SETD3, actin, and viral 2A during virus replication. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8x8q.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8x8q.ent.gz | 102.5 KB | Display | PDB format |
PDBx/mmJSON format | 8x8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8x8q_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8x8q_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8x8q_validation.xml.gz | 31 KB | Display | |
Data in CIF | 8x8q_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/8x8q ftp://data.pdbj.org/pub/pdb/validation_reports/x8/8x8q | HTTPS FTP |
-Related structure data
Related structure data | 38156MC 8x77C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 67342.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETD3 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q86TU7 |
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#2: Protein | Mass: 16562.418 Da / Num. of mol.: 1 / Mutation: C110A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterovirus A71 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: R9YK28 |
#3: Chemical | ChemComp-ZN / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: enterovirus protease in complex host factor / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: Baculovirus expression vector pFastBac1-HM | ||||||||||||
Buffer solution | pH: 8 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1800 nm / Calibrated defocus min: 1800 nm / Calibrated defocus max: 2500 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 70 K |
Image recording | Electron dose: 66 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Particle selection | Num. of particles selected: 2211651 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 603524 / Num. of class averages: 66 / Symmetry type: POINT |
Atomic model building | B value: 103 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient |
Atomic model building | PDB-ID: 3w95 Accession code: 3w95 / Source name: PDB / Type: experimental model |