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- EMDB-26069: Coxsackievirus A21 capsid subdomain in complex with mouse polyclo... -

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Basic information

Entry
Database: EMDB / ID: EMD-26069
TitleCoxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-2
Map datacryoEM map of the subdomain of CV-A21 viral particle in complex with mouse polyclonal antibody pAbC-2 - Main map
Sample
  • Complex: Immune complex featuring subdomains of coxsackievirus A21 (CV-A21) viral particles in complex with mouse polyclonal antibodies
    • Protein or peptide: Coxsackievirus capsid - Polyprotein
    • Protein or peptide: pAbC-2
Keywordspolyclonal antibodies / Immunology / viral particles / VIRUS-IMMUNE SYSTEM complex
Biological speciesCoxsackievirus A21 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsAntanasijevic A / Ward AB
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: PNAS Nexus / Year: 2022
Title: High-resolution structural analysis of enterovirus-reactive polyclonal antibodies in complex with whole virions.
Authors: Aleksandar Antanasijevic / Autumn J Schulze / Vijay S Reddy / Andrew B Ward /
Abstract: Non-polio enteroviruses (NPEVs) cause serious illnesses in young children and neonates, including aseptic meningitis, encephalitis, and inflammatory muscle disease, among others. While over 100 ...Non-polio enteroviruses (NPEVs) cause serious illnesses in young children and neonates, including aseptic meningitis, encephalitis, and inflammatory muscle disease, among others. While over 100 serotypes have been described to date, vaccine only exists for EV-A71. Efforts toward rationally designed pan-NPEV vaccines would greatly benefit from structural biology methods for rapid and comprehensive evaluation of vaccine candidates and elicited antibody responses. Toward this goal, we introduced a cryo-electron-microscopy-based approach for structural analysis of virus- or vaccine-elicited polyclonal antibodies (pAbs) in complex with whole NPEV virions. We demonstrated the feasibility using coxsackievirus A21 and reconstructed five structurally distinct pAbs bound to the virus. The pAbs targeted two immunodominant epitopes, one overlapping with the receptor binding site. These results demonstrate that our method can be applied to map broad-spectrum polyclonal immune responses against intact virions and define potentially cross-reactive epitopes.
History
DepositionJan 26, 2022-
Header (metadata) releaseJan 4, 2023-
Map releaseJan 4, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26069.png

Downloads & links

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Map

FileDownload / File: emd_26069.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoEM map of the subdomain of CV-A21 viral particle in complex with mouse polyclonal antibody pAbC-2 - Main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 280 pix.
= 292.6 Å		1.05 Å/pix.
x 280 pix.
= 292.6 Å		1.05 Å/pix.
x 280 pix.
= 292.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.005642439 - 0.011850693
Average (Standard dev.)0.00026527714 (±0.00077717484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 292.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26069_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoEM map of the subdomain of CV-A21 viral...

Fileemd_26069_half_map_1.map
AnnotationcryoEM map of the subdomain of CV-A21 viral particle in complex with mouse polyclonal antibody pAbC-2 - Half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoEM map of the subdomain of CV-A21 viral...

Fileemd_26069_half_map_2.map
AnnotationcryoEM map of the subdomain of CV-A21 viral particle in complex with mouse polyclonal antibody pAbC-2 - Half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Immune complex featuring subdomains of coxsackievirus A21 (CV-A21...

EntireName: Immune complex featuring subdomains of coxsackievirus A21 (CV-A21) viral particles in complex with mouse polyclonal antibodies
Components
  • Complex: Immune complex featuring subdomains of coxsackievirus A21 (CV-A21) viral particles in complex with mouse polyclonal antibodies
    • Protein or peptide: Coxsackievirus capsid - Polyprotein
    • Protein or peptide: pAbC-2

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Supramolecule #1: Immune complex featuring subdomains of coxsackievirus A21 (CV-A21...

SupramoleculeName: Immune complex featuring subdomains of coxsackievirus A21 (CV-A21) viral particles in complex with mouse polyclonal antibodies
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The complexes were assembled by combining purified CV-A21 particles and polyclonal antibodies isolated from mice (as Fab fragments)
Source (natural)Organism: Coxsackievirus A21

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Macromolecule #1: Coxsackievirus capsid - Polyprotein

MacromoleculeName: Coxsackievirus capsid - Polyprotein / type: protein_or_peptide / ID: 1
Details: CV-A21 capsid polyprotein sequence is provided. The sequence includes VP1-4.
Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A21
SequenceString: MGAQVSTQKT GAHENQNVAA NGSTINYTTI NYYKDSASNS ATRQDLSQDP SKFTEPVKDL MLKTAPALNS PNVEACGYSD RVRQITLGNS TITTQEAANA IVAYGEWPTY INDSEANPVD APTEPDVSSN RFYTLESVSW KTTSRGWWWK LPDCLKDMGM FGQNMYYHYL ...String:
MGAQVSTQKT GAHENQNVAA NGSTINYTTI NYYKDSASNS ATRQDLSQDP SKFTEPVKDL MLKTAPALNS PNVEACGYSD RVRQITLGNS TITTQEAANA IVAYGEWPTY INDSEANPVD APTEPDVSSN RFYTLESVSW KTTSRGWWWK LPDCLKDMGM FGQNMYYHYL GRSGYTIHVQ CNASKFHQGA LGVFLIPEFV MACNTESKTS YVSYINANPG ERGGEFTNTY NPSNTDASEG RKFAALDYLL GSGVLAGNAF VYPHQIINLR TNNSATIVVP YVNSLVIDCM AKHNNWGIVI LPLAPLAFAA TSSPQVPITV TIAPMCTEFN GLRNITVPVH QGLPTMNTPG SNQFLTSDDF QSPCALPNFD VTPPIHIPGE VKNMMELAEI DTLIPMNAVD GKVNTMEMYQ IPLNDNLSKA PIFCLSLSPA SDKRLSHTML GEILNYYTHW TGSIRFTFLF CGSMMATGKL LLSYSPPGAK PPTNRKDAML GTHIIWDLGL QSSCSMVAPW ISNTVYRRCA RDDFTEGGFI TCFYQTRIVV PASTPTSMFM LGFVSACPDF SVRLLRDTPH ISQSKLIGRT QGIEDLIDTA IKNALRVSQP PSTQSTEATS GVNSQEVPAL TAVETGASGQ AIPSDVVETR HVVNYKTRSE SCLESFFGRA ACVTILSLTN SSKSGEEKKH FNIWNITYTD TVQLRRKLEF FTYSRFDLEM TFVFTENYPS TASGEVRNQV YQIMYIPPGA PRPSSWDDYT WQSSSNPSIF YMYGNAPPRM SIPYVGIANA YSHFYDGFAR VPLEGENTDA GDTFYGLVSI NDFGVLAVRA VNRSNPHTIH TSVRVYMKPK HIRCWCPRPP RAVLYRGEGV DMISSAILPL AKVDSITTF

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Macromolecule #2: pAbC-2

MacromoleculeName: pAbC-2 / type: protein_or_peptide / ID: 2 / Details: Polyclonal antibody pAbC-2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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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

Concentration2.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
10.0 mMTris-HClTris
150.0 mMNaClSodium Chloride

Details: TBS
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time varied: 3-5s.
DetailsImmune complexes were SEC-purified, concentrated and applied onto cryo-grids.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 3862 / Average exposure time: 9.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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

DetailsFrames aligned using MotionCor2
Particle selectionNumber selected: 22937
Details: Template picker. Particles were 2D cleaned and symmetry expanded (icosahedral symmetry). Sym-expanded particles were used for 3D classification and refinement.
Startup modelType of model: OTHER / Details: low-pass filtered map of CV-A21
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Details: 7792 symmetry expanded particles / Number images used: 7792
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0) / Details: regularized likelihood
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0) / Details: regularized likelihood
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.0)
Details: 3D classifications were performed without image alignment.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1z7s


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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