[English] 日本語
Yorodumi
- EMDB-33225: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33225
TitleCryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Map dataCryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsGeorge FG / Sheng L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell / Year: 2022
Title: Protective prototype-Beta and Delta-Omicron chimeric RBD-dimer vaccines against SARS-CoV-2.
Authors: Kun Xu / Ping Gao / Sheng Liu / Shuaiyao Lu / Wenwen Lei / Tianyi Zheng / Xueyuan Liu / Yufeng Xie / Zhennan Zhao / Shuxin Guo / Cong Tang / Yun Yang / Wenhai Yu / Junbin Wang / Yanan Zhou / ...Authors: Kun Xu / Ping Gao / Sheng Liu / Shuaiyao Lu / Wenwen Lei / Tianyi Zheng / Xueyuan Liu / Yufeng Xie / Zhennan Zhao / Shuxin Guo / Cong Tang / Yun Yang / Wenhai Yu / Junbin Wang / Yanan Zhou / Qing Huang / Chuanyu Liu / Yaling An / Rong Zhang / Yuxuan Han / Minrun Duan / Shaofeng Wang / Chenxi Yang / Changwei Wu / Xiaoya Liu / Guangbiao She / Yan Liu / Xin Zhao / Ke Xu / Jianxun Qi / Guizhen Wu / Xiaozhong Peng / Lianpan Dai / Peiyi Wang / George F Gao /
Abstract: Breakthrough infections by SARS-CoV-2 variants become the global challenge for pandemic control. Previously, we developed the protein subunit vaccine ZF2001 based on the dimeric receptor-binding ...Breakthrough infections by SARS-CoV-2 variants become the global challenge for pandemic control. Previously, we developed the protein subunit vaccine ZF2001 based on the dimeric receptor-binding domain (RBD) of prototype SARS-CoV-2. Here, we developed a chimeric RBD-dimer vaccine approach to adapt SARS-CoV-2 variants. A prototype-Beta chimeric RBD-dimer was first designed to adapt the resistant Beta variant. Compared with its homotypic forms, the chimeric vaccine elicited broader sera neutralization of variants and conferred better protection in mice. The protection of the chimeric vaccine was further verified in macaques. This approach was generalized to develop Delta-Omicron chimeric RBD-dimer to adapt the currently prevalent variants. Again, the chimeric vaccine elicited broader sera neutralization of SARS-CoV-2 variants and conferred better protection against challenge by either Delta or Omicron SARS-CoV-2 in mice. The chimeric approach is applicable for rapid updating of immunogens, and our data supported the use of variant-adapted multivalent vaccine against circulating and emerging variants.
History
DepositionApr 17, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateMay 3, 2023-
Current statusMay 3, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33225.png

Downloads & links

-
Map

FileDownload / File: emd_33225.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Voxel sizeX=Y=Z: 0.66 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.111364536 - 0.23417038
Average (Standard dev.)-0.00011597294 (±0.018531024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 211.20001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab

Fileemd_33225_half_map_1.map
AnnotationCryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab

Fileemd_33225_half_map_2.map
AnnotationCryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab

EntireName: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab

-
Supramolecule #1: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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 / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.39 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26842

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more