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- EMDB-70397: Structure of the human astrovirus VA1 capsid spike bound to antib... -

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Basic information

Entry
Database: EMDB / ID: EMD-70397
TitleStructure of the human astrovirus VA1 capsid spike bound to antibody 7C8
Map dataMain refined and sharpened map
Sample
  • Complex: Human astrovirus VA1 capsid spike bound to antibody 7C8
    • Protein or peptide: Spike protein VP38
    • Protein or peptide: 7C8 heavy chain
    • Protein or peptide: 7C8 light chain
KeywordsAstrovirus / neutralizing antibody / epitope mapping / neurovirulent. / VIRAL PROTEIN
Function / homologyCapsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / T=3 icosahedral viral capsid / Viral coat protein subunit / clathrin-dependent endocytosis of virus by host cell / Capsid polyprotein VP86
Function and homology information
Biological speciesAstrovirus VA1 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsGhosh A / Dzimianski JV / Balasco Serrao VH / DuBois RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI144090 United States
CitationJournal: To Be Published
Title: Cryo-EM Structures of the Human Astrovirus VA1 Capsid Spike Bound to Neutralizing Antibodies: Implications for Therapeutic Strategies
Authors: Ghosh A / Dzimianski JV / Lopez T / Espinosa R / Balasco Serrao VH / Arias CF / DuBois RM
History
DepositionApr 28, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70397.png

Downloads & links

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Map

FileReleased
AnnotationMain refined and sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.152
Minimum - Maximum-0.87731546 - 1.2226236
Average (Standard dev.)-0.00013168555 (±0.027943406)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70397_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Original half map B before particle subtraction

Fileemd_70397_additional_1.map
AnnotationOriginal half map B before particle subtraction
Projections & Slices
AxesZYX

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Additional map: Original half map A before particle subtraction

Fileemd_70397_additional_2.map
AnnotationOriginal half map A before particle subtraction
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Additional map: Unsharpened map

Fileemd_70397_additional_3.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Original map before particle subtraction

Fileemd_70397_additional_4.map
AnnotationOriginal map before particle subtraction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B

Fileemd_70397_half_map_1.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A

Fileemd_70397_half_map_2.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Sample components

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Entire : Human astrovirus VA1 capsid spike bound to antibody 7C8

EntireName: Human astrovirus VA1 capsid spike bound to antibody 7C8
Components
  • Complex: Human astrovirus VA1 capsid spike bound to antibody 7C8
    • Protein or peptide: Spike protein VP38
    • Protein or peptide: 7C8 heavy chain
    • Protein or peptide: 7C8 light chain

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Supramolecule #1: Human astrovirus VA1 capsid spike bound to antibody 7C8

SupramoleculeName: Human astrovirus VA1 capsid spike bound to antibody 7C8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Astrovirus VA1

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Macromolecule #1: Spike protein VP38

MacromoleculeName: Spike protein VP38 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Astrovirus VA1
Molecular weightTheoretical: 32.219271 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGPIPPTGVP VGDFFVCGRM TTLHMGGQSG IQATTLVNGM IYRTDHPEPS SSPVSNWEFT VLENNTIVGA GMGCVWFQKS EALVWTLDG QKLSGWNTLD GVGTTQLTVA WRQHNRTIYG WANVVAWNSE EWHTNAEQPH QPILRLTYWL VKINVLSEPE D FDVVQKSP ...String:
MGPIPPTGVP VGDFFVCGRM TTLHMGGQSG IQATTLVNGM IYRTDHPEPS SSPVSNWEFT VLENNTIVGA GMGCVWFQKS EALVWTLDG QKLSGWNTLD GVGTTQLTVA WRQHNRTIYG WANVVAWNSE EWHTNAEQPH QPILRLTYWL VKINVLSEPE D FDVVQKSP LAYLEDYTTA QSKSAIQKLN FQTFQKPEGG GTLRAQYSTT PRQGDFAVIW QIGRHNFDMS TGKGTPVESL SD YVMPQQK DAHIGMWYRA LTSVGPRTDV LTLHFHLPTV EKAAAELALV PR

UniProtKB: Capsid polyprotein VP86

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Macromolecule #2: 7C8 heavy chain

MacromoleculeName: 7C8 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.465312 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLVESGGG LVKPGGSLKL SCAASGFTFS DYYMYWIRQT PEKRLEWVAT ISDGGFSTYY PDSVKGRFTI SRDNAKNNLF LQMSSLKSE DTAIYYCARF GAYSTFWGQQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
EVQLVESGGG LVKPGGSLKL SCAASGFTFS DYYMYWIRQT PEKRLEWVAT ISDGGFSTYY PDSVKGRFTI SRDNAKNNLF LQMSSLKSE DTAIYYCARF GAYSTFWGQQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK S

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Macromolecule #3: 7C8 light chain

MacromoleculeName: 7C8 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.466078 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QIVLSQSPAI LSASPGEKVT MTCRASSSVS YMYWYQQQKP GSPKPWIYAT SNLASGVPAR FSGSGSGTSY SLTIISRVEA EDATYYCQQ WSSDPPMTFG GGTTKLEIKR RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
QIVLSQSPAI LSASPGEKVT MTCRASSSVS YMYWYQQQKP GSPKPWIYAT SNLASGVPAR FSGSGSGTSY SLTIISRVEA EDATYYCQQ WSSDPPMTFG GGTTKLEIKR RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGE

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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

Concentration1 mg/mL
BufferpH: 8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7270 / Average electron dose: 34.14 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 135000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3598944
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 211718
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8ufo

chain_id: A, source_name: PDB, initial_model_type: experimental model

8ufo

chain_id: C, source_name: PDB, initial_model_type: experimental model
chain_id: H, source_name: SwissModel, initial_model_type: in silico model
chain_id: J, source_name: SwissModel, initial_model_type: in silico model
chain_id: L, source_name: SwissModel, initial_model_type: in silico model
chain_id: K, source_name: SwissModel, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9oef:
Structure of the human astrovirus VA1 capsid spike bound to antibody 7C8

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