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- EMDB-31733: cryo-EM map focused on interface between 3E8 and ACE2 -

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Basic information

Entry
Database: EMDB / ID: EMD-31733
Titlecryo-EM map focused on interface between 3E8 and ACE2
Map datacryo-EM map focused on interface between 3E8 and ACE2
Sample
  • Complex: cryo-EM map focused on interface between 3E8 and ACE2
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYan RH / Zhang YY
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
National Natural Science Foundation of China (NSFC)81920108015 China
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Signal Transduct Target Ther / Year: 2021
Title: ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker.
Authors: Yuning Chen / Ya-Nan Zhang / Renhong Yan / Guifeng Wang / Yuanyuan Zhang / Zhe-Rui Zhang / Yaning Li / Jianxia Ou / Wendi Chu / Zhijuan Liang / Yongmei Wang / Yi-Li Chen / Ganjun Chen / Qi ...Authors: Yuning Chen / Ya-Nan Zhang / Renhong Yan / Guifeng Wang / Yuanyuan Zhang / Zhe-Rui Zhang / Yaning Li / Jianxia Ou / Wendi Chu / Zhijuan Liang / Yongmei Wang / Yi-Li Chen / Ganjun Chen / Qi Wang / Qiang Zhou / Bo Zhang / Chunhe Wang /
Abstract: The evolution of coronaviruses, such as SARS-CoV-2, makes broad-spectrum coronavirus preventional or therapeutical strategies highly sought after. Here we report a human angiotensin-converting enzyme ...The evolution of coronaviruses, such as SARS-CoV-2, makes broad-spectrum coronavirus preventional or therapeutical strategies highly sought after. Here we report a human angiotensin-converting enzyme 2 (ACE2)-targeting monoclonal antibody, 3E8, blocked the S1-subunits and pseudo-typed virus constructs from multiple coronaviruses including SARS-CoV-2, SARS-CoV-2 mutant variants (SARS-CoV-2-D614G, B.1.1.7, B.1.351, B.1.617.1, and P.1), SARS-CoV and HCoV-NL63, without markedly affecting the physiological activities of ACE2 or causing severe toxicity in ACE2 "knock-in" mice. 3E8 also blocked live SARS-CoV-2 infection in vitro and in a prophylactic mouse model of COVID-19. Cryo-EM and "alanine walk" studies revealed the key binding residues on ACE2 interacting with the CDR3 domain of 3E8 heavy chain. Although full evaluation of safety in non-human primates is necessary before clinical development of 3E8, we provided a potentially potent and "broad-spectrum" management strategy against all coronaviruses that utilize ACE2 as entry receptors and disclosed an anti-coronavirus epitope on human ACE2.
History
DepositionAug 18, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31733.png

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Map

FileDownload / File: emd_31733.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map focused on interface between 3E8 and ACE2
Voxel sizeX=Y=Z: 1.077 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.046307188 - 0.087748505
Average (Standard dev.)0.00025670504 (±0.0021309173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 310.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : cryo-EM map focused on interface between 3E8 and ACE2

EntireName: cryo-EM map focused on interface between 3E8 and ACE2
Components
  • Complex: cryo-EM map focused on interface between 3E8 and ACE2

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Supramolecule #1: cryo-EM map focused on interface between 3E8 and ACE2

SupramoleculeName: cryo-EM map focused on interface between 3E8 and ACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 203324

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