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- EMDB-26072: Coxsackievirus A21 capsid subdomain in complex with mouse polyclo... -

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Basic information

Entry
Database: EMDB / ID: EMD-26072
TitleCoxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1
Map dataCoxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1 - Main Map
Sample
  • Complex: Immune complex featuring subdomains of coxsackievirus A21 (CV-A21) viral particles in complex with mouse polyclonal antibodies
    • Protein or peptide: pAbC-1 heavy chain
    • Protein or peptide: pAbC-1 light chain
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
  • Ligand: MYRISTIC ACID
Function / homology
Function and homology information


: / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell ...: / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesCoxsackievirus A21 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 27, 2022-
Header (metadata) releaseJan 4, 2023-
Map releaseJan 4, 2023-
UpdateFeb 8, 2023-
Current statusFeb 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26072.png

Downloads & links

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Map

FileDownload / File: emd_26072.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCoxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1 - Main Map
Voxel sizeX=Y=Z: 1.045 Å
Density
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.018071491 - 0.027934082
Average (Standard dev.)0.00020931913 (±0.0021467127)
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_26072_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Coxsackievirus A21 capsid subdomain in complex with mouse...

Fileemd_26072_half_map_1.map
AnnotationCoxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1 - Half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Coxsackievirus A21 capsid subdomain in complex with mouse...

Fileemd_26072_half_map_2.map
AnnotationCoxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1 - 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: pAbC-1 heavy chain
    • Protein or peptide: pAbC-1 light chain
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
  • Ligand: MYRISTIC ACID

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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 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#6
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: pAbC-1 heavy chain

MacromoleculeName: pAbC-1 heavy chain / type: protein_or_peptide / ID: 1 / Details: Heavy Chain of the polyclonal antibody pAbC-1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 9.549763 KDa
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)

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Macromolecule #2: pAbC-1 light chain

MacromoleculeName: pAbC-1 light chain / type: protein_or_peptide / ID: 2 / Details: Light Chain of the polyclonal antibody pAbC-1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 8.698714 KDa
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)

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Macromolecule #3: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 3 / Details: VP1 protein of the coxsackievirus A21 capsid / Number of copies: 3 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus A21
Molecular weightTheoretical: 33.234238 KDa
SequenceString: GIEDLIDTAI KNALRVSQPP STQSTEATSG VNSQEVPALT AVETGASGQA IPSDVVETRH VVNYKTRSES CLESFFGRAA CVTILSLTN SSKSGEEKKH FNIWNITYTD TVQLRRKLEF FTYSRFDLEM TFVFTENYPS TASGEVRNQV YQIMYIPPGA P RPSSWDDY ...String:
GIEDLIDTAI KNALRVSQPP STQSTEATSG VNSQEVPALT AVETGASGQA IPSDVVETRH VVNYKTRSES CLESFFGRAA CVTILSLTN SSKSGEEKKH FNIWNITYTD TVQLRRKLEF FTYSRFDLEM TFVFTENYPS TASGEVRNQV YQIMYIPPGA P RPSSWDDY TWQSSSNPSI FYMYGNAPPR MSIPYVGIAN AYSHFYDGFA RVPLEGENTD AGDTFYGLVS INDFGVLAVR AV NRSNPHT IHTSVRVYMK PKHIRCWCPR PPRAVLYRGE GVDMISSAIL PLAKVDSITT F

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Macromolecule #4: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 4 / Details: VP2 protein of the coxsackievirus A21 capsid / Number of copies: 3 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus A21
Molecular weightTheoretical: 29.918537 KDa
SequenceString: SPNVEACGYS DRVRQITLGN STITTQEAAN AIVAYGEWPT YINDSEANPV DAPTEPDVSS NRFYTLESVS WKTTSRGWWW KLPDCLKDM GMFGQNMYYH YLGRSGYTIH VQCNASKFHQ GALGVFLIPE FVMACNTESK TSYVSYINAN PGERGGEFTN T YNPSNTDA ...String:
SPNVEACGYS DRVRQITLGN STITTQEAAN AIVAYGEWPT YINDSEANPV DAPTEPDVSS NRFYTLESVS WKTTSRGWWW KLPDCLKDM GMFGQNMYYH YLGRSGYTIH VQCNASKFHQ GALGVFLIPE FVMACNTESK TSYVSYINAN PGERGGEFTN T YNPSNTDA SEGRKFAALD YLLGSGVLAG NAFVYPHQII NLRTNNSATI VVPYVNSLVI DCMAKHNNWG IVILPLAPLA FA ATSSPQV PITVTIAPMC TEFNGLRNIT VPVHQ

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Macromolecule #5: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 5 / Details: VP3 protein of the coxsackievirus A21 capsid / Number of copies: 3 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus A21
Molecular weightTheoretical: 26.596703 KDa
SequenceString: GLPTMNTPGS NQFLTSDDFQ SPCALPNFDV TPPIHIPGEV KNMMELAEID TLIPMNAVDG KVNTMEMYQI PLNDNLSKAP IFCLSLSPA SDKRLSHTML GEILNYYTHW TGSIRFTFLF CGSMMATGKL LLSYSPPGAK PPTNRKDAML GTHIIWDLGL Q SSCSMVAP ...String:
GLPTMNTPGS NQFLTSDDFQ SPCALPNFDV TPPIHIPGEV KNMMELAEID TLIPMNAVDG KVNTMEMYQI PLNDNLSKAP IFCLSLSPA SDKRLSHTML GEILNYYTHW TGSIRFTFLF CGSMMATGKL LLSYSPPGAK PPTNRKDAML GTHIIWDLGL Q SSCSMVAP WISNTVYRRC ARDDFTEGGF ITCFYQTRIV VPASTPTSMF MLGFVSACPD FSVRLLRDTP HISQSKLIGR TQ

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Macromolecule #6: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 6 / Details: VP4 protein of the coxsackievirus A21 capsid / Number of copies: 3 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus A21
Molecular weightTheoretical: 7.442118 KDa
SequenceString:
MGAQVSTQKT GAHENQNVAA NGSTINYTTI NYYKDSASNS ATRQDLSQDP SKFTEPVKDL MLKTAPALN

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Macromolecule #7: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 7 / Number of copies: 3 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID / Myristic acid

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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-HClTrisTris-HClTris
150.0 mMNaClSodium chlorideSodium chloride

Details: TBS, 0.2um filtered
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: 10 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: 3-7s blot time.
DetailsThe complex was generated by incubation of mouse polyclonal antibodies with recombinantly expressed CV-A21 virions and subsequent SEC purification.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 22937
Details: Cryosparc template picker. Following the 2D classification and symmetry expansion the number of particles was 1334700. Symmetry-expanded particles were used for 3D classification and refinement.
Startup modelType of model: OTHER / Details: Low-pass filtered map of coxsackievirus particle
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0) / Details: Relion, regularized likelihood
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.0) / Details: 3D classification without image alignment
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0) / Details: Relion, regularized likelihood
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Details: 19748 symmetry-expanded particles / Number images used: 19748
DetailsMotionCor2 was used for frame alignment
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1z7s

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7tqu:
Coxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1

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