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- PDB-7n62: SARS-CoV-2 Spike (2P) in complex with C12C9 Fab (NTD local recons... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n62 | ||||||
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Title | SARS-CoV-2 Spike (2P) in complex with C12C9 Fab (NTD local reconstruction) | ||||||
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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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Windsor, I.W. / Jenni, S. / Bajic, G. / Tong, P. / Gautam, A.K. / Wesemann, D.R. / Harrison, S.C. | ||||||
![]() | ![]() 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, A.K. / Windsor, I.W. / Bajic, G. / Harrison, S.C. / Wesemann, D.R. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.1 KB | Display | ![]() |
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PDB format | ![]() | 115.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 24192MC ![]() 7n64C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | ![]() Mass: 141297.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2 / Production host: ![]() ![]() | ||
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#2: Antibody | Mass: 24556.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Antibody | Mass: 23235.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#4: Sugar | ChemComp-NAG / ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: SARS-CoV-2 Spike in complex with 12-C9 Fab / Type: COMPLEX 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. Entity ID: #1-#3 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() ![]() ![]() | |||||||||||||||
Source (recombinant) | Organism: ![]() ![]() ![]() | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||
Vitrification![]() | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 88 % / Chamber temperature: 298 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1.8 sec. / Electron dose: 54.97 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2842883 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147461 / Num. of class averages: 8 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 141.24 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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