[English] 日本語
Yorodumi
- EMDB-31438: SARS-CoV-2 S trimer in complex with 2 A34-2 Fabs (2 RBDs open and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31438
TitleSARS-CoV-2 S trimer in complex with 2 A34-2 Fabs (2 RBDs open and 1 RBD close)
Map data
Sample
  • Complex: SARS-CoV-2 S trimer in complex with 2 A34-2 Fabs (2 RBDs open and 1 RBD close)
KeywordsSARS-CoV-2 / S / Fab / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsDou Y / Wang X / Liu P / Wang K / Lu B
CitationJournal: Antib Ther / Year: 2023
Title: Development of neutralizing antibodies against SARS-CoV-2, using a high-throughput single-B-cell cloning method.
Authors: Yang Dou / Ke Xu / Yong-Qiang Deng / Zijing Jia / Jun Lan / Xiaoyu Xu / Guorui Zhang / Tianshu Cao / Pan Liu / Xiangxi Wang / Xinquan Wang / Lingjie Xu / Pan Du / Cheng-Feng Qin / Hong Liu / ...Authors: Yang Dou / Ke Xu / Yong-Qiang Deng / Zijing Jia / Jun Lan / Xiaoyu Xu / Guorui Zhang / Tianshu Cao / Pan Liu / Xiangxi Wang / Xinquan Wang / Lingjie Xu / Pan Du / Cheng-Feng Qin / Hong Liu / Yafeng Li / Guizhen Wu / Kang Wang / Bai Lu /
Abstract: BACKGROUND: Rapid and efficient strategies are needed to discover neutralizing antibodies (nAbs) from B cells derived from virus-infected patients.
METHODS: Here, we report a high-throughput single-B-cell cloning method for high-throughput isolation of nAbs targeting diverse epitopes on the SARS-CoV-2-RBD (receptor binding domain) from ...METHODS: Here, we report a high-throughput single-B-cell cloning method for high-throughput isolation of nAbs targeting diverse epitopes on the SARS-CoV-2-RBD (receptor binding domain) from convalescent COVID-19 patients. This method is simple, fast and highly efficient in generating SARS-CoV-2-neutralizing antibodies from COVID-19 patients' B cells.
RESULTS: Using this method, we have developed multiple nAbs against distinct SARS-CoV-2-RBD epitopes. CryoEM and crystallography revealed precisely how they bind RBD. In live virus assay, these nAbs ...RESULTS: Using this method, we have developed multiple nAbs against distinct SARS-CoV-2-RBD epitopes. CryoEM and crystallography revealed precisely how they bind RBD. In live virus assay, these nAbs are effective in blocking viral entry to the host cells.
CONCLUSION: This simple and efficient method may be useful in developing human therapeutic antibodies for other diseases and next pandemic.
History
DepositionJun 16, 2021-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_31438.png

Downloads & links

-
Map

FileDownload / File: emd_31438.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.08 Å/pix.
x 200 pix.
= 416. Å		2.08 Å/pix.
x 200 pix.
= 416. Å		2.08 Å/pix.
x 200 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.03681364 - 0.15078376
Average (Standard dev.)0.0003747342 (±0.0040091695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : SARS-CoV-2 S trimer in complex with 2 A34-2 Fabs (2 RBDs open and...

EntireName: SARS-CoV-2 S trimer in complex with 2 A34-2 Fabs (2 RBDs open and 1 RBD close)
Components
  • Complex: SARS-CoV-2 S trimer in complex with 2 A34-2 Fabs (2 RBDs open and 1 RBD close)

-
Supramolecule #1: SARS-CoV-2 S trimer in complex with 2 A34-2 Fabs (2 RBDs open and...

SupramoleculeName: SARS-CoV-2 S trimer in complex with 2 A34-2 Fabs (2 RBDs open and 1 RBD close)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 173964
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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