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- EMDB-60933: Cryo-EM structure of the CHIKV nsP3 peptide in complex with the N... -

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Basic information

Entry
Database: EMDB / ID: EMD-60933
TitleCryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1 (Conformation II)
Map data
Sample
  • Complex: CHIKV nsP3 in complex with human G3BP1
    • Protein or peptide: Ras GTPase-activating protein-binding protein 1
    • Protein or peptide: Polyprotein P1234
KeywordsChikungunya virus / nsP3 / G3BP1 / protein-protein interaction. / VIRAL PROTEIN
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 / DNA helicase / methylation / defense response to virus / perikaryon / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / Ras protein signal transduction / four-way junction helicase activity / double-stranded DNA helicase activity / RNA helicase activity / RNA helicase / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / viral RNA genome replication / DNA clamp loader activity / innate immune response / focal adhesion / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase activity / DNA-templated transcription / mRNA binding / host cell nucleus / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / ATP binding / nucleus / metal ion binding / 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 / Macro domain profile. / 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 speciesChikungunya virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWang J / Liu YZ / Lei J / Wang KT
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFF0702004 China
Ministry of Science and Technology (MoST, China)2022YFC2303701 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1
Authors: Liu YZ / Wang J / Wang KT / Lei J
History
DepositionJul 24, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60933.png

Downloads & links

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Map

FileDownload / File: emd_60933.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 320 pix.
= 232. Å		0.73 Å/pix.
x 320 pix.
= 232. Å		0.73 Å/pix.
x 320 pix.
= 232. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0477
Minimum - Maximum-0.10992613 - 0.20979775
Average (Standard dev.)0.00008739129 (±0.008394512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 232.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60933_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_60933_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : CHIKV nsP3 in complex with human G3BP1

EntireName: CHIKV nsP3 in complex with human G3BP1
Components
  • Complex: CHIKV nsP3 in complex with human G3BP1
    • Protein or peptide: Ras GTPase-activating protein-binding protein 1
    • Protein or peptide: Polyprotein P1234

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Supramolecule #1: CHIKV nsP3 in complex with human G3BP1

SupramoleculeName: CHIKV nsP3 in complex with human G3BP1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chikungunya virus

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Macromolecule #1: Ras GTPase-activating protein-binding protein 1

MacromoleculeName: Ras GTPase-activating protein-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.057231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GASMVMEKPS PLLVGREFVR QYYTLLNQAP DMLHRFYGKN SSYVHGGLDS NGKPADAVYG QKEIHRKVMS QNFTNCHTKI RHVDAHATL NDGVVVQVMG LLSNNNQALR RFMQTFVLAP EGSVANKFYV HNDIFRYQDE VF

UniProtKB: Ras GTPase-activating protein-binding protein 1

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Macromolecule #2: Polyprotein P1234

MacromoleculeName: Polyprotein P1234 / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus
Molecular weightTheoretical: 6.000295 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPLGSETFPI TFGDFNDGEI ESLSSELLTF GDFLPGEVDD LTDSDWSTHH HHHH

UniProtKB: Polyprotein P1234

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: OTHER
Details: The value given for _em_vitrification.instrument is CRYOSOL VITROJET. This is not in a list of allowed values {'GATAN CRYOPLUNGE 3', 'REICHERT-JUNG PLUNGER', 'LEICA KF80', 'SPOTITON', 'FEI ...Details: The value given for _em_vitrification.instrument is CRYOSOL VITROJET. This is not in a list of allowed values {'GATAN CRYOPLUNGE 3', 'REICHERT-JUNG PLUNGER', 'LEICA KF80', 'SPOTITON', 'FEI VITROBOT MARK IV', 'OTHER', 'HOMEMADE PLUNGER', 'LEICA EM GP', 'LEICA EM CPC', 'FEI VITROBOT MARK III', 'FEI VITROBOT MARK I', 'LEICA PLUNGER', 'EMS-002 RAPID IMMERSION FREEZER', 'FEI VITROBOT MARK II'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 296402
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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