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- EMDB-39260: Cryo-EM structure of partial VP4 from simian rotavirus SA11 -

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Basic information

Entry
Database: EMDB / ID: EMD-39260
TitleCryo-EM structure of partial VP4 from simian rotavirus SA11
Map data
Sample
  • Virus: Rotavirus A
    • Complex: Partial VP4 of rotavirus
      • Protein or peptide: Outer capsid protein VP4
      • Protein or peptide: Outer capsid protein VP4
      • Protein or peptide: Outer capsid protein VP4
KeywordsVIRUS / ROTAVIRUS / VP4
Function / homology
Function and homology information


host cytoskeleton / viral outer capsid / symbiont entry into host cell via permeabilization of host membrane / host cell endoplasmic reticulum / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus A
Methodsingle particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsHuang Y / Sun H / Zheng Q / Li S / Ge S / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: A single residue switch mediates the broad neutralization of Rotaviruses.
Authors: Yang Huang / Feibo Song / Yuanjun Zeng / Hui Sun / Roufang Sheng / Xuechun Wang / Liqin Liu / Guoxing Luo / Yanan Jiang / Yaling Chen / Mengxuan Zhang / Shiyin Zhang / Ying Gu / Hai Yu / ...Authors: Yang Huang / Feibo Song / Yuanjun Zeng / Hui Sun / Roufang Sheng / Xuechun Wang / Liqin Liu / Guoxing Luo / Yanan Jiang / Yaling Chen / Mengxuan Zhang / Shiyin Zhang / Ying Gu / Hai Yu / Shaowei Li / Tingdong Li / Qingbing Zheng / Shengxiang Ge / Jun Zhang / Ningshao Xia /
Abstract: Broadly neutralizing antibodies (bNAbs) could offer escape-tolerant and lasting protection against viral infections and therefore guide development of broad-spectrum vaccines. The increasing ...Broadly neutralizing antibodies (bNAbs) could offer escape-tolerant and lasting protection against viral infections and therefore guide development of broad-spectrum vaccines. The increasing challenge posed by viral evolution and immune evasion intensifies the importance of the discovery of bNAbs and their underlying neutralization mechanism. Here, focusing on the pivotal viral protein VP4 of rotavirus (RV), we identify a potent bNAb, 7H13, exhibiting broad-spectrum neutralization across diverse RV genotypes and demonstrating strong prevention of virus infection in female mice. A combination of time-resolved cryo-electron microscopy (cryo-EM) and in situ cryo-electron tomography (cryo-ET) analysis reveals a counterintuitive dynamic process of virus inactivation, in which 7H13 asymmetrically binds to a conserved epitope in the capsid-proximal aspect of VP4, triggers a conformational switch in a critical residue-F418-thereby disrupts the meta-stable conformation of VP4 essential for normal viral infection. Structure-guided mutagenesis corroborates the essential role of the 7H13 heavy chain I54 in activating F418 switch and destabilizing VP4. These findings define an atypical NAbs' neutralization mechanism and reveal a potential type of virus vulnerable site for universal vaccine and therapeutics design.
History
DepositionFeb 26, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39260.png

Downloads & links

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Map

FileDownload / File: emd_39260.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 360 pix.
= 360. Å		1 Å/pix.
x 360 pix.
= 360. Å		1 Å/pix.
x 360 pix.
= 360. Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0018588144 - 2.5111344
Average (Standard dev.)0.00074242224 (±0.01986414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39260_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_39260_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Rotavirus A

EntireName: Rotavirus A
Components
  • Virus: Rotavirus A
    • Complex: Partial VP4 of rotavirus
      • Protein or peptide: Outer capsid protein VP4
      • Protein or peptide: Outer capsid protein VP4
      • Protein or peptide: Outer capsid protein VP4

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Supramolecule #1: Rotavirus A

SupramoleculeName: Rotavirus A / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 28875 / Sci species name: Rotavirus A / Sci species strain: SA11 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Supramolecule #2: Partial VP4 of rotavirus

SupramoleculeName: Partial VP4 of rotavirus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Rotavirus A / Strain: SA11

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Macromolecule #1: Outer capsid protein VP4

MacromoleculeName: Outer capsid protein VP4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus A / Strain: SA11
Molecular weightTheoretical: 64.861418 KDa
SequenceString: GYKMASLIYR QLLTNSYTVD LSDEIQEIGS TKSQNVTINP GPFAQTGYAP VNWGPGEIND STTVEPLLDG PYQPTTFNPP VDYWMLLAP TTPGVIVEGT NNTDRWLATI LIEPNVQSEN RTYTIFGIQE QLTVSNTSQD QWKFIDVVKT TANGSIGQYG P LLSSPKLY ...String:
GYKMASLIYR QLLTNSYTVD LSDEIQEIGS TKSQNVTINP GPFAQTGYAP VNWGPGEIND STTVEPLLDG PYQPTTFNPP VDYWMLLAP TTPGVIVEGT NNTDRWLATI LIEPNVQSEN RTYTIFGIQE QLTVSNTSQD QWKFIDVVKT TANGSIGQYG P LLSSPKLY AVMKHNEKLY TYEGQTPNAR TAHYSTTNYD SVNMTAFCDF YIIPRSEESK CTEYINNGLP PIQNTRNVVP LS LTARDVI HYRAQANEDI VISKTSLWKE MQYNRDITIR FKFANTIIKS GGLGYKWSEI SFKPANYQYT YTRDGEEVTA HTT CSVNGV NDFSFNGGSL PTDFVVSKFE VIKENSYVYI DYWDDSQAFR NVVYVRSLAA NLNSVMCTGG SYNFSLPVGQ WPVL TGGAV SLHSAGVTLS TQFTDFVSLN SLRFRFRLAV EEPHFKLTRT RLSRLYGLPA ANPNNGKEYY EIAGRFSLIS LVPSN HDYQ TPIANSVTVR QDLERQLGEL REEFNALSQE IAMSQLIDLA LLPLDMFSMF SGIKSTIDAA KSMATNVMKK FKKSGL ANS VSTLTDSLSD AASSISRG

UniProtKB: Outer capsid protein VP4

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Macromolecule #2: Outer capsid protein VP4

MacromoleculeName: Outer capsid protein VP4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus A / Strain: SA11
Molecular weightTheoretical: 64.889465 KDa
SequenceString: GYKMASLIYR QLLTNSYTVD LSDEIQEIGS TKSQNVTINP GPFAQTGYAP VNWGPGEIND STTVEPLLDG PYQPTTFNPP VDYWMLLAP TTPGVIVEGT NNTDRWLATI LIEPNVQSEN RTYTIFGIQE QLTVSNTSQD QWKFIDVVKT TANGSIGQYG P LLSSPKLY ...String:
GYKMASLIYR QLLTNSYTVD LSDEIQEIGS TKSQNVTINP GPFAQTGYAP VNWGPGEIND STTVEPLLDG PYQPTTFNPP VDYWMLLAP TTPGVIVEGT NNTDRWLATI LIEPNVQSEN RTYTIFGIQE QLTVSNTSQD QWKFIDVVKT TANGSIGQYG P LLSSPKLY AVMKHNEKLY TYEGQTPNAR TAHYSTTNYD SVNMTAFCDF YIIPRSEESK CTEYINNGLP PIQNTRNVVP LS LTARDVI HYRAQVNEDI VISKTSLWKE MQYNRDITIR FKFANTIIKS GGLGYKWSEI SFKPANYQYT YTRDGEEVTA HTT CSVNGV NDFSFNGGSL PTDFVVSKFE VIKENSYVYI DYWDDSQAFR NVVYVRSLAA NLNSVMCTGG SYNFSLPVGQ WPVL TGGAV SLHSAGVTLS TQFTDFVSLN SLRFRFRLAV EEPHFKLTRT RLSRLYGLPA ANPNNGKEYY EIAGRFSLIS LVPSN HDYQ TPIANSVTVR QDLERQLGEL REEFNALSQE IAMSQLIDLA LLPLDMFSMF SGIKSTIDAA KSMATNVMKK FKKSGL ANS VSTLTDSLSD AASSISRG

UniProtKB: Outer capsid protein VP4

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Macromolecule #3: Outer capsid protein VP4

MacromoleculeName: Outer capsid protein VP4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus A / Strain: SA11
Molecular weightTheoretical: 64.891465 KDa
SequenceString: GYKMASLIYR QLLTNSYTVD LSDEIQEIGS TKSQNVTINP GPFAQTGYAP VNWGPGEIND STTVEPLLDG PYQPTTFNPP VDYWMLLAP TTPGVIVEGT NNTDRWLATI LIEPNVQSEN RTYTIFGIQE QLTVSNTSQD QWKFIDVAKT TANGSIEQYG P LLSSPKLY ...String:
GYKMASLIYR QLLTNSYTVD LSDEIQEIGS TKSQNVTINP GPFAQTGYAP VNWGPGEIND STTVEPLLDG PYQPTTFNPP VDYWMLLAP TTPGVIVEGT NNTDRWLATI LIEPNVQSEN RTYTIFGIQE QLTVSNTSQD QWKFIDVAKT TANGSIEQYG P LLSSPKLY AVMKHNKKLY TYEGQTPNAR TGHYSTTNYD SVNMTAFCDF YIIPRSEESK CTEYINNGLP PIQNTRNVVP LS LTARDVI HYRAQANEDI VISKTSLWKE MQYNRDITIR FKFANTIIKS GGLGYKWSEI SFKPANYQYT YTRDGEEVTA HTT CSVNGV NDFSFNGGSL PTDFVVSKFE VIKENSYVYI DYWDDSQAFR NVVYVRSLAA NLNSVMCTGG SYNFSLPVGQ WPVL TGGAV SLHSAGVTLS TQFTDFVSLN SLRFRFRLAV EEPHFKLTRT RLSRLYGLPA ANPNNGKEYY EIAGRFSLIS LVPSN HDYQ TPIANSVTVR QDLERQLGEL REEFNALSQE IAMSQLIDLA LLPLDMFSMF SGIKSTIDAA KSMATNVMKK FKKSGL ANS VSTLTDSLSD AASSISRG

UniProtKB: Outer capsid protein VP4

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 367118
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: cryosparc local refine
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: cryosparc local refine

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