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- PDB-9ivs: Cryo-EM structure of the CHIKV nsP3 peptide in complex with the N... -

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Basic information

Entry
Database: PDB / ID: 9ivs
TitleCryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1 (Conformation III)
Components
  • Polyprotein P1234
  • Ras GTPase-activating protein-binding protein 1
KeywordsVIRAL PROTEIN / Chikungunya virus / nsP3 / G3BP1 / protein-protein interaction.
Function / homology
Function and homology information


DNA/RNA helicase activity / positive regulation of stress granule assembly / host cell filopodium / mRNA methyltransferase activity / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / ribosomal small subunit binding / 7-methylguanosine mRNA capping ...DNA/RNA helicase activity / positive regulation of stress granule assembly / host cell filopodium / mRNA methyltransferase activity / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / mRNA modification / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / ribosomal small subunit binding / 7-methylguanosine mRNA capping / positive regulation of type I interferon production / DNA helicase activity / stress granule assembly / cysteine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / negative regulation of canonical Wnt signaling pathway / molecular condensate scaffold activity / host cell cytoplasmic vesicle membrane / cytoplasmic stress granule / endonuclease activity / methylation / defense response to virus / DNA helicase / perikaryon / Ras protein signal transduction / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host gene expression / innate immune response / viral RNA genome replication / focal adhesion / RNA-directed RNA polymerase activity / DNA-templated transcription / mRNA binding / GTP binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
G3BP1, RNA recognition motif / Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 ...G3BP1, RNA recognition motif / Ras GTPase-activating protein-binding protein / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / Alphavirus nsp2 protease (nsp2pro) domain / Alphavirus nsP2 protease domain superfamily / : / Peptidase family C9 / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsp2 protease (nsp2pro) domain profile. / : / Non-structural protein 3, zinc-binding domain / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / NTF2-like domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Nucleotide-binding alpha-beta plait domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Polyprotein P1234 / Ras GTPase-activating protein-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Chikungunya virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsWang, J. / Liu, Y.Z. / Lei, J. / Wang, K.T.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFF0702004 China
Ministry of Science and Technology (MoST, China)2022YFC2303701 China
CitationJournal: mBio / Year: 2025
Title: Cryo-EM reveals a double oligomeric ring scaffold of the CHIKV nsP3 peptide in complex with the NTF2L domain of host G3BP1.
Authors: Yuanzhi Liu / Jie Wang / Yinze Han / Xiaoyan Xia / Rui Zeng / Xinyu Fan / Bo Zhang / Kaituo Wang / Jian Lei /
Abstract: Chikungunya virus (CHIKV) poses a severe threat to global public health. The interaction between CHIKV nsP3 and host G3BP1 is critical for viral replication. However, the exact structural mechanism ...Chikungunya virus (CHIKV) poses a severe threat to global public health. The interaction between CHIKV nsP3 and host G3BP1 is critical for viral replication. However, the exact structural mechanism of the nsP3-G3BP1 interaction is scarce. Here, we report a cryo-electron microscopy structure of an octameric-heterotrimer formed by CHIKV nsP3 peptide (designated as CHIKV-43) in complex with the nuclear translocation factor 2-like (NTF2L) domain of G3BP1. The overall structure presents a double-layer ring scaffold. Two FGDF motifs and two alpha helices of CHIKV-43 are essential to bind NTF2L. Particularly, the secondary alpha helix plays key roles in forming the CHIKV-43-NTF2L high-order oligomer. We next analyzed the detailed interactions between CHIKV-43 and the NTF2L domain. The different binding patterns of NTF2L with its various partners were described as well. Subsequently, we demonstrated that the CHIKV-43 peptide is a crucial factor for nsP3 co-localization with G3BP1, reducing stress granule formation and interfering with interferon production. Overall, our findings present the structural and functional mechanisms on CHIKV nsP3 modulating host G3BP1 and provide a potential antiviral target based on the protein-protein interaction interface.
IMPORTANCE: Chikungunya virus (CHIKV) is an arbovirus responsible for causing fever, headache, and severe joint pain in humans, with widespread outbreaks affecting millions worldwide. The CHIKV nsP3 ...IMPORTANCE: Chikungunya virus (CHIKV) is an arbovirus responsible for causing fever, headache, and severe joint pain in humans, with widespread outbreaks affecting millions worldwide. The CHIKV nsP3 is a key protein that interacts with multiple host proteins. In this study, we present the cryo-electron microscopy structure of a high-order oligomer formed by the CHIKV nsP3 peptide and the nuclear translocation factor 2-like (NTF2L) domain of host protein G3BP1, revealing a completely novel interaction model. The detailed interactions within this oligomer were illustrated. We also analyzed the binding patterns of the NTF2L domain of G3BP1 with its various partners, providing essential insights for the development of peptide-mimetic inhibitors targeting nsP3 and/or G3BP1. Furthermore, our data indicate that the nsP3-G3BP1 interaction reduces stress granule formation and antagonizes interferon production. Overall, this study provides new knowledge on CHIKV biology and suggests a potential target for developing antiviral therapeutics.
History
DepositionJul 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras GTPase-activating protein-binding protein 1
C: Ras GTPase-activating protein-binding protein 1
D: Ras GTPase-activating protein-binding protein 1
B: Ras GTPase-activating protein-binding protein 1
L: Polyprotein P1234
I: Polyprotein P1234
P: Ras GTPase-activating protein-binding protein 1
N: Ras GTPase-activating protein-binding protein 1
M: Ras GTPase-activating protein-binding protein 1
O: Ras GTPase-activating protein-binding protein 1
V: Polyprotein P1234
U: Polyprotein P1234
T: Ras GTPase-activating protein-binding protein 1
R: Ras GTPase-activating protein-binding protein 1
Q: Ras GTPase-activating protein-binding protein 1
S: Ras GTPase-activating protein-binding protein 1
X: Polyprotein P1234
W: Polyprotein P1234
E: Ras GTPase-activating protein-binding protein 1
G: Ras GTPase-activating protein-binding protein 1
H: Ras GTPase-activating protein-binding protein 1
F: Ras GTPase-activating protein-binding protein 1
J: Polyprotein P1234
K: Polyprotein P1234


Theoretical massNumber of molelcules
Total (without water)304,91824
Polymers304,91824
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Ras GTPase-activating protein-binding protein 1 / G3BP1-NTF2 / G3BP-1 / ATP-dependent DNA helicase VIII / hDH VIII / GAP SH3 domain-binding protein 1


Mass: 16057.231 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G3BP1, G3BP / Production host: Escherichia coli (E. coli) / References: UniProt: Q13283, DNA helicase, RNA helicase
#2: Protein
Polyprotein P1234 / nsP3 peptide / Non-structural polyprotein


Mass: 6000.295 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U5KFN5
Has protein modificationN

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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: CHIKV nsP3 in complex with human G3BP1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Chikungunya virus37124
31Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: CRYOSOL VITROJET / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161792 / Symmetry type: POINT
RefinementHighest resolution: 2.97 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00720238
ELECTRON MICROSCOPYf_angle_d1.03627373
ELECTRON MICROSCOPYf_dihedral_angle_d5.1042697
ELECTRON MICROSCOPYf_chiral_restr0.0462907
ELECTRON MICROSCOPYf_plane_restr0.0073642

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