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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24198 | |||||||||
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Title | SARS-CoV-2 spike (2P) in complex with C12A2 Fab | |||||||||
![]() | SARS-CoV-2 spike (2P) in complex with C12A2 Fab | |||||||||
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Function / homology | ![]() Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Bajic G / Windsor IW / Tong P / Gautam A / Wesemann DR / Harrison SC | |||||||||
![]() | ![]() Title: Memory B cell repertoire for recognition of evolving SARS-CoV-2 spike. Authors: Pei Tong / Avneesh Gautam / Ian Windsor / Meghan Travers / Yuezhou Chen / Nicholas Garcia / Noah B Whiteman / Lindsay G A McKay / Felipe J N Lelis / Shaghayegh Habibi / Yongfei Cai / Linda J ...Authors: Pei Tong / Avneesh Gautam / Ian Windsor / Meghan Travers / Yuezhou Chen / Nicholas Garcia / Noah B Whiteman / Lindsay G A McKay / Felipe J N Lelis / Shaghayegh Habibi / Yongfei Cai / Linda J Rennick / W Paul Duprex / Kevin R McCarthy / Christy L Lavine / Teng Zuo / Junrui Lin / Adam Zuiani / Jared Feldman / Elizabeth A MacDonald / Blake M Hauser / Anthony Griffths / Michael S Seaman / Aaron G Schmidt / Bing Chen / Donna Neuberg / Goran Bajic / Stephen C Harrison / Duane R Wesemann / ![]() Abstract: Memory B cell reserves can generate protective antibodies against repeated SARS-CoV-2 infections, but with an unknown reach from original infection to antigenically drifted variants. We charted ...Memory B cell reserves can generate protective antibodies against repeated SARS-CoV-2 infections, but with an unknown reach from original infection to antigenically drifted variants. We charted memory B cell receptor-encoded monoclonal antibodies (mAbs) from 19 COVID-19 convalescent subjects against SARS-CoV-2 spike (S) and found 7 major mAb competition groups against epitopes recurrently targeted across individuals. Inclusion of published and newly determined structures of mAb-S complexes identified corresponding epitopic regions. Group assignment correlated with cross-CoV-reactivity breadth, neutralization potency, and convergent antibody signatures. mAbs that competed for binding the original S isolate bound differentially to S variants, suggesting the protective importance of otherwise-redundant recognition. The results furnish a global atlas of the S-specific memory B cell repertoire and illustrate properties conferring robustness against emerging SARS-CoV-2 variants. #1: ![]() Title: Memory B Cell Repertoire for Recognition of Evolving SARS-CoV-2 Spike Authors: Tong P / Gautam AK / Windsor IW / Bajic G / Harrison SC / Wesemann DR | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 155.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13 KB 13 KB | Display Display | ![]() |
Images | ![]() | 101.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 346.2 KB | Display | ![]() |
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Full document | ![]() | 345.8 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | SARS-CoV-2 spike (2P) in complex with C12A2 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : SARS-CoV-2 spike (2P) in complex with C12A2 Fab
Entire | Name: SARS-CoV-2 spike (2P) in complex with C12A2 Fab |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike (2P) in complex with C12A2 Fab
Supramolecule | Name: SARS-CoV-2 spike (2P) in complex with C12A2 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: B cell receptor was sequenced from memory B cell of SARS-CoV-2 convalescent human patient and express as Fab. SARS-CoV2-2 surface protein (with 2P stabilizing mutations) was expressed as soluble ectodomain. |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 / Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 88 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 54.01 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.2 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |