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- EMDB-70398: Structure of the human astrovirus VA1 capsid spike bound to antib... -

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Basic information

Entry
Database: EMDB / ID: EMD-70398
TitleStructure of the human astrovirus VA1 capsid spike bound to antibody 2A2
Map dataMain sharpened map
Sample
  • Complex: Human astrovirus VA1 capsid spike bound to antibody 2A2
    • Protein or peptide: 2A2 heavy chain
    • Protein or peptide: 2A2 light chain
    • Protein or peptide: Capsid polyprotein VP90
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: 3.05 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_70398.png

Downloads & links

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Map

FileReleased
AnnotationMain sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 288 pix.
= 231.168 Å		0.8 Å/pix.
x 288 pix.
= 231.168 Å		0.8 Å/pix.
x 288 pix.
= 231.168 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.80267 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.365
Minimum - Maximum-2.323067 - 2.9602976
Average (Standard dev.)0.00013201193 (±0.065250486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 231.16801 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70398_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Unsharpened map

Fileemd_70398_additional_1.map
AnnotationUnsharpened map
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Additional map: Spisonet corrected half map A

Fileemd_70398_additional_2.map
AnnotationSpisonet corrected half map A
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Additional map: Spisonet corrected half map B

Fileemd_70398_additional_3.map
AnnotationSpisonet corrected half map B
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Additional map: Unsharpened map before particle subtraction

Fileemd_70398_additional_4.map
AnnotationUnsharpened map before particle subtraction
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AxesZYX

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Additional map: Halpf map A before particle subtraction

Fileemd_70398_additional_5.map
AnnotationHalpf map A before particle subtraction
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Additional map: Half map B before particle subtraction

Fileemd_70398_additional_6.map
AnnotationHalf map B before particle subtraction
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AxesZYX

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Half map: Half map A

Fileemd_70398_half_map_1.map
AnnotationHalf map A
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Histogram

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Half map: Half map B

Fileemd_70398_half_map_2.map
AnnotationHalf map B
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Sample components

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Entire : Human astrovirus VA1 capsid spike bound to antibody 2A2

EntireName: Human astrovirus VA1 capsid spike bound to antibody 2A2
Components
  • Complex: Human astrovirus VA1 capsid spike bound to antibody 2A2
    • Protein or peptide: 2A2 heavy chain
    • Protein or peptide: 2A2 light chain
    • Protein or peptide: Capsid polyprotein VP90

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Supramolecule #1: Human astrovirus VA1 capsid spike bound to antibody 2A2

SupramoleculeName: Human astrovirus VA1 capsid spike bound to antibody 2A2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Astrovirus VA1

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Macromolecule #1: 2A2 heavy chain

MacromoleculeName: 2A2 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.010914 KDa
SequenceString: DVQLVESGGG LVQPGGSRKL SCAASGFTFS YFGMHWVRQA PEKGLEWVAY ISSGSNTIYY ADTVKGRFTI SRDNPKNTLF LQMTSLRSE DTAMYYCARA YYGNHYYAMD FWGPGTSVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
DVQLVESGGG LVQPGGSRKL SCAASGFTFS YFGMHWVRQA PEKGLEWVAY ISSGSNTIYY ADTVKGRFTI SRDNPKNTLF LQMTSLRSE DTAMYYCARA YYGNHYYAMD FWGPGTSVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSC

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Macromolecule #2: 2A2 light chain

MacromoleculeName: 2A2 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.727322 KDa
SequenceString: DIQMTQSPAS LSVSVGETVT ITCRASENIY SNLAWYQQKR GKSPQLLVHA ARDLATGVPS RFSGSGSGTQ YSLKINSLQS EDFGTYYCQ HFWETPWTFG GGTKLEIKRR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPAS LSVSVGETVT ITCRASENIY SNLAWYQQKR GKSPQLLVHA ARDLATGVPS RFSGSGSGTQ YSLKINSLQS EDFGTYYCQ HFWETPWTFG GGTKLEIKRR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #3: Capsid polyprotein VP90

MacromoleculeName: Capsid polyprotein VP90 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Astrovirus VA1
Molecular weightTheoretical: 32.233299 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGPIPPTGVP VGDFFVCGRM TTLHMGGQSG IQATTLVNGM IYRTDHPEPS TSPVSNWEFT VLENNTIVGA GMGCVWFQKS EALVWTLDG QKLSGWNTLD GVGTTQLTVA WRQHNRTIYG WANVVAWNSE EWHTNAEQPH QPILRLTYWL VKINVLSEPE D FDVVQKSP ...String:
MGPIPPTGVP VGDFFVCGRM TTLHMGGQSG IQATTLVNGM IYRTDHPEPS TSPVSNWEFT 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.9 mg/mL
BufferpH: 8
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: 6902 / Average electron dose: 19.92 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: 1527268
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 166364
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: B, 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-9oeg:
Structure of the human astrovirus VA1 capsid spike bound to antibody 2A2

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