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- EMDB-29227: cryoEM structure of a broadly neutralizing antibody STI-9167 -

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Basic information

Entry
Database: EMDB / ID: EMD-29227
TitlecryoEM structure of a broadly neutralizing antibody STI-9167
Map datanon-sharpened map
Sample
  • Complex: SARS-CoV-2 spike RBD in complex with 10A3 Fab
Keywordsantibody / SARS-CoV-2 / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsBajic G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI168178 United States
CitationJournal: mBio / Year: 2024
Title: An experimental pipeline to characterize the epitope of a SARS-CoV-2 neutralizing antibody.
Authors: Kristina E Atanasoff / Luca Brambilla / Daniel C Adelsberg / Shreyas Kowdle / Christian S Stevens / Stefan Slamanig / Chuan-Tien Hung / Yanwen Fu / Reyna Lim / Linh Tran / Robert Allen / ...Authors: Kristina E Atanasoff / Luca Brambilla / Daniel C Adelsberg / Shreyas Kowdle / Christian S Stevens / Stefan Slamanig / Chuan-Tien Hung / Yanwen Fu / Reyna Lim / Linh Tran / Robert Allen / Weina Sun / J Andrew Duty / Goran Bajic / Benhur Lee / Domenico Tortorella /
Abstract: The COVID-19 pandemic remains a significant public health concern for the global population; the development and characterization of therapeutics, especially ones that are broadly effective, will ...The COVID-19 pandemic remains a significant public health concern for the global population; the development and characterization of therapeutics, especially ones that are broadly effective, will continue to be essential as severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) variants emerge. Neutralizing monoclonal antibodies remain an effective therapeutic strategy to prevent virus infection and spread so long as they recognize and interact with circulating variants. The epitope and binding specificity of a neutralizing anti-SARS-CoV-2 Spike receptor-binding domain antibody clone against many SARS-CoV-2 variants of concern were characterized by generating antibody-resistant virions coupled with cryo-EM structural analysis and VSV-spike neutralization studies. This workflow can serve to predict the efficacy of antibody therapeutics against emerging variants and inform the design of therapeutics and vaccines.
History
DepositionDec 19, 2022-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29227.png

Downloads & links

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Map

FileDownload / File: emd_29227.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnon-sharpened map
Voxel sizeX=Y=Z: 0.826 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.2877342 - 1.3883259
Average (Standard dev.)-0.0010825811 (±0.033198528)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 422.912 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhancer sharpened map

Fileemd_29227_additional_1.map
AnnotationDeepEMhancer sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryoSPARC sharpened map

Fileemd_29227_additional_2.map
AnnotationcryoSPARC sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_29227_half_map_1.map
Annotationhalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 1

Fileemd_29227_half_map_2.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 spike RBD in complex with 10A3 Fab

EntireName: SARS-CoV-2 spike RBD in complex with 10A3 Fab
Components
  • Complex: SARS-CoV-2 spike RBD in complex with 10A3 Fab

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Supramolecule #1: SARS-CoV-2 spike RBD in complex with 10A3 Fab

SupramoleculeName: SARS-CoV-2 spike RBD in complex with 10A3 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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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

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.92 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6m0j

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 320574
FSC plot (resolution estimation)

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