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Yorodumi- EMDB-26069: Coxsackievirus A21 capsid subdomain in complex with mouse polyclo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26069 | |||||||||
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Title | Coxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-2 | |||||||||
Map data | cryoEM map of the subdomain of CV-A21 viral particle in complex with mouse polyclonal antibody pAbC-2 - Main map | |||||||||
Sample |
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Keywords | polyclonal antibodies / Immunology / viral particles / VIRUS-IMMUNE SYSTEM complex | |||||||||
Biological species | Coxsackievirus A21 / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Antanasijevic A / Ward AB | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26069.map.gz | 76.1 MB | EMDB map data format | |
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Header (meta data) | emd-26069-v30.xml emd-26069.xml | 21.3 KB 21.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26069_fsc.xml | 10.1 KB | Display | FSC data file |
Images | emd_26069.png | 79.7 KB | ||
Masks | emd_26069_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-26069.cif.gz | 6 KB | ||
Others | emd_26069_half_map_1.map.gz emd_26069_half_map_2.map.gz | 65.2 MB 65.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26069 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26069 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26069.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | cryoEM map of the subdomain of CV-A21 viral particle in complex with mouse polyclonal antibody pAbC-2 - Main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26069_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: cryoEM map of the subdomain of CV-A21 viral...
File | emd_26069_half_map_1.map | ||||||||||||
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Annotation | cryoEM map of the subdomain of CV-A21 viral particle in complex with mouse polyclonal antibody pAbC-2 - Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryoEM map of the subdomain of CV-A21 viral...
File | emd_26069_half_map_2.map | ||||||||||||
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Annotation | cryoEM map of the subdomain of CV-A21 viral particle in complex with mouse polyclonal antibody pAbC-2 - Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Immune complex featuring subdomains of coxsackievirus A21 (CV-A21...
Entire | Name: Immune complex featuring subdomains of coxsackievirus A21 (CV-A21) viral particles in complex with mouse polyclonal antibodies |
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Components |
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-Supramolecule #1: Immune complex featuring subdomains of coxsackievirus A21 (CV-A21...
Supramolecule | Name: 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) |
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Source (natural) | Organism: Coxsackievirus A21 |
-Macromolecule #1: Coxsackievirus capsid - Polyprotein
Macromolecule | Name: Coxsackievirus capsid - Polyprotein / type: protein_or_peptide / ID: 1 Details: CV-A21 capsid polyprotein sequence is provided. The sequence includes VP1-4. Enantiomer: LEVO |
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Source (natural) | Organism: Coxsackievirus A21 |
Sequence | String: 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 |
-Macromolecule #2: pAbC-2
Macromolecule | Name: pAbC-2 / type: protein_or_peptide / ID: 2 / Details: Polyclonal antibody pAbC-2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Sequence | 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) ...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) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: TBS | |||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time varied: 3-5s. | |||||||||
Details | Immune complexes were SEC-purified, concentrated and applied onto cryo-grids. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film 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 |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |