[English] 日本語
Yorodumi
- PDB-9j5s: Crystal structure of human G3BP1 in complex with CHIKV nsP3 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j5s
TitleCrystal structure of human G3BP1 in complex with CHIKV nsP3 peptide
Components
  • Polyprotein P1234
  • Ras GTPase-activating protein-binding protein 1
KeywordsVIRAL PROTEIN / chikungunya virus / non-structural protein / virus-host interaction
Function / homology
Function and homology information


DNA/RNA helicase activity / 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/RNA helicase activity / 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 / cysteine-type peptidase activity / stress granule assembly / DNA helicase activity / molecular condensate scaffold activity / ribonucleoside triphosphate phosphatase activity / negative regulation of canonical Wnt signaling pathway / host cell cytoplasmic vesicle membrane / cytoplasmic stress granule / endonuclease activity / methylation / perikaryon / defense response to virus / DNA helicase / Ras protein signal transduction / 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 / mRNA binding / DNA-templated transcription / 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 core domain / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsLiu, Y.Z. / Lei, J.
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
DepositionAug 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras GTPase-activating protein-binding protein 1
B: Ras GTPase-activating protein-binding protein 1
C: Polyprotein P1234
D: Polyprotein P1234


Theoretical massNumber of molelcules
Total (without water)37,8434
Polymers37,8434
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-26 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.506, 71.450, 53.517
Angle α, β, γ (deg.)90.00, 95.64, 90.00
Int Tables number5
Space group name H-MC121

-
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.: 2
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/peptide Polyprotein P1234 / Non-structural polyprotein


Mass: 2864.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Chikungunya virus / References: UniProt: A0A0U5KFN5
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20%(w/v) PEG 3350, 200mM Sodium citrate tribasic, 100mM Sodium citrate/Citric acid pH 4.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.84→36.19 Å / Num. obs: 8074 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.76 / Net I/σ(I): 4
Reflection shellResolution: 2.85→2.92 Å / Num. unique obs: 605 / CC1/2: 0.435

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FW5

5fw5


Resolution: 2.84→36.19 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2804 407 5.05 %
Rwork0.226 --
obs0.2289 8065 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.84→36.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 0 0 2320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012371
X-RAY DIFFRACTIONf_angle_d1.4523196
X-RAY DIFFRACTIONf_dihedral_angle_d16.838310
X-RAY DIFFRACTIONf_chiral_restr0.076340
X-RAY DIFFRACTIONf_plane_restr0.008421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-3.250.35031240.26622543X-RAY DIFFRACTION99
3.25-4.10.34281280.23562548X-RAY DIFFRACTION100
4.1-36.190.21761550.20012567X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more