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- EMDB-36223: Cryo-EM structure of the GI.4 Chiba VLP complexed with the CV-1A1... -

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Basic information

Entry
Database: EMDB / ID: EMD-36223
TitleCryo-EM structure of the GI.4 Chiba VLP complexed with the CV-1A1 Fv-clasp
Map data
Sample
  • Complex: Viral protein 1 with its antibody fragments
    • Protein or peptide: VP1
    • Protein or peptide: VH,SARAH
    • Protein or peptide: VL,SARAH
KeywordsNOROVIRUS / GI.4 / VIRUS LIKE PARTICLE / human monoclonal antibody / Fv-clasp / VIRUS
Biological speciesChiba virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsHosaka T / Katsura K / Kimura-Someya T / Someya Y / Shirouzu M
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21fk0108121 Japan
Japan Agency for Medical Research and Development (AMED)JP22fk0108121 Japan
CitationJournal: J Virol / Year: 2024
Title: Structural analyses of the GI.4 norovirus by cryo-electron microscopy and X-ray crystallography revealing binding sites for human monoclonal antibodies.
Authors: Tomomi Kimura-Someya / Kazushige Katsura / Miyuki Kato-Murayama / Toshiaki Hosaka / Tomomi Uchikubo-Kamo / Kentaro Ihara / Kazuharu Hanada / Shin Sato / Kazutaka Murayama / Michiyo Kataoka / ...Authors: Tomomi Kimura-Someya / Kazushige Katsura / Miyuki Kato-Murayama / Toshiaki Hosaka / Tomomi Uchikubo-Kamo / Kentaro Ihara / Kazuharu Hanada / Shin Sato / Kazutaka Murayama / Michiyo Kataoka / Mikako Shirouzu / Yuichi Someya /
Abstract: Noroviruses are major causative agents of acute nonbacterial gastroenteritis in humans. There are neither antiviral therapeutic agents nor vaccines for noroviruses at this time. To evaluate the ...Noroviruses are major causative agents of acute nonbacterial gastroenteritis in humans. There are neither antiviral therapeutic agents nor vaccines for noroviruses at this time. To evaluate the potential usefulness of two previously isolated human monoclonal antibody fragments, CV-1A1 and CV-2F5, we first conducted a single-particle analysis to determine the cryo-electron microscopy structure of virus-like particles (VLPs) from the genogroup I genotype 4 (GI.4) Chiba strain uniformly coated with CV-1A1 fragments. The results revealed that the GI.4-specific CV-1A1 antibody bound to the P2 subdomain, in which amino acids are less conserved and variable. Interestingly, a part of the CV-1A1 intrudes into the histo-blood group antigen-binding site, suggesting that this antibody might exert neutralizing activity. Next, we determined the crystal structure of the protruding (P) domain of the capsid protein in the complex form with the CV-2F5 antibody fragment. Consistent with the cross-reactivity, the CV-2F5 bound to the P1 subdomain, which is rich in amino acids conserved among the GI strains, and moreover induced a disruption of Chiba VLPs. These results suggest that the broadly reactive CV-2F5 antibody can be used as both a universal detection reagent and an antiviral drug for GI noroviruses.
IMPORTANCE: We conducted the structural analyses of the VP1 protein from the GI.4 Chiba norovirus to identify the binding sites of the previously isolated human monoclonal antibodies CV-1A1 and CV- ...IMPORTANCE: We conducted the structural analyses of the VP1 protein from the GI.4 Chiba norovirus to identify the binding sites of the previously isolated human monoclonal antibodies CV-1A1 and CV-2F5. The cryo-electron microscopy of the Chiba virus-like particles (VLPs) complexed with the Fv-clasp forms of GI.4-specific CV-1A1 revealed that this antibody binds to the highly variable P2 subdomain, suggesting that this antibody may have neutralizing ability against the GI.4 strains. X-ray crystallography revealed that the CV-2F5 antibody bound to the P1 subdomain, which is rich in conserved amino acids. This result is consistent with the ability of the CV-2F5 antibody to react with a wide variety of GI norovirus strains. It is also found that the CV-2F5 antibody caused a disruption of VLPs. Our findings, together with previous reports on the structures of VP1 proteins and VLPs, are expected to open a path for the structure-based development of antivirals and vaccines against norovirus disease.
History
DepositionMay 19, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36223.png

Downloads & links

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Map

FileDownload / File: emd_36223.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.47 Å/pix.
x 500 pix.
= 735. Å		1.47 Å/pix.
x 500 pix.
= 735. Å		1.47 Å/pix.
x 500 pix.
= 735. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.47 Å
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Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.5610304 - 3.3488245
Average (Standard dev.)0.004567188 (±0.12802236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 735.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36223_msk_1.map
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Additional map: #1

Fileemd_36223_additional_1.map
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Half map: #1

Fileemd_36223_half_map_1.map
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Half map: #2

Fileemd_36223_half_map_2.map
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Sample components

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Entire : Viral protein 1 with its antibody fragments

EntireName: Viral protein 1 with its antibody fragments
Components
  • Complex: Viral protein 1 with its antibody fragments
    • Protein or peptide: VP1
    • Protein or peptide: VH,SARAH
    • Protein or peptide: VL,SARAH

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Supramolecule #1: Viral protein 1 with its antibody fragments

SupramoleculeName: Viral protein 1 with its antibody fragments / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chiba virus / Strain: GI/Human/Japan/Chiba 407/1987

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Details: GenBank ID AB042808 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chiba virus / Strain: GI/Human/Japan/Chiba 407/1987
Molecular weightTheoretical: 58.108332 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASKDATPSA DGATGAGQLV PEVNTADPIP IDPVAGSSTA APVAGQVNLI DPWIINNFVQ APQGEFTISP NNTPGDVLFD LQLGPHLNP FLSHLSQMYN GWVGNMRVRV VLAGNAFTAG KVIICCVPPG FQSRTLSIAQ ATLFPHVIAD VRTLDPVEVP L EDVRNVLY ...String:
MASKDATPSA DGATGAGQLV PEVNTADPIP IDPVAGSSTA APVAGQVNLI DPWIINNFVQ APQGEFTISP NNTPGDVLFD LQLGPHLNP FLSHLSQMYN GWVGNMRVRV VLAGNAFTAG KVIICCVPPG FQSRTLSIAQ ATLFPHVIAD VRTLDPVEVP L EDVRNVLY HNNDTQPTMR LLCMLYTPLR TGGASGGTDS FVVAGRVLTC PGPDFNFLFL VPPTVEQKTR PFTVPNIPLK YL SNSRIPN PIEGMSLSPD QTQNVQFQNG RCTIDGQPLG TTPVSVSQLC KFRGRITSGQ RVLNLTELDG SPFMAFAAPA PAG FPDLGS CDWHIEMSKI PNSSTQNNPI VTNSVKPNSQ QFVPHLSSIT LDENVSSGGD YIGTIQWTSP PSDSGGANTN FWKI PDYGS SLAEASQLAP AVYPPGFNEV IVYFMASIPG PNQSGSPNLV PCLLPQEYIT HFISEQAPIQ GEAALLHYVD PDTNR NLGE FKLYPGGYLT CVPNSSSTGP QQLPLDGVFV FASWVSRFYQ LKPVGTAGPA RGRLGVRR

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Macromolecule #2: VH,SARAH

MacromoleculeName: VH,SARAH / type: protein_or_peptide / ID: 2
Details: VH-SARAH chimera of linker (residues (-6)-0), VH (residues 1-118), and SARAH (residues 119-171)
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.847254 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSSGSSGEVQ LVESGAEVKK PGASVKVSCK ASGYTFTSLY MHWVRQAPGQ GLEWMGMINP SGGGTWNAQK FQGRVTMTRD TSTSTVYME LRSLRSDDTA MYYCARDSDQ YSQGLGYWGQ GTLVTVCSGS DYEFLKSWTV EDLQKRLLAL DPMMEQEIEE I RQKYQSKR QPILDAIEAK

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Macromolecule #3: VL,SARAH

MacromoleculeName: VL,SARAH / type: protein_or_peptide / ID: 3
Details: VL-SARAH chimera of linker (residues (-6)-0), VL (residues 1-112), and SARAH (residues 113-162)
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.19315 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSSGSSGQSA LTQPASVSGS PGQSITISCT GTSSDVGGYN YVSWYQQHPG KAPKLMIYDV SKRPSGVSNR FSGSKSGNTA SLTISGLQA KDEADYYCSS YTSSSTWVFG GGTKLTVLGG SDYEFLKSWT VEDLQKRLLA LDPMMEQEIE EIRQKYQCKR Q PILDAIEA K

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6out

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47125
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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