[English] 日本語
Yorodumi
- EMDB-77347: Cryo-EM global density map of BA.4-S/Ab#10-M30W-S94M IgG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-77347
TitleCryo-EM global density map of BA.4-S/Ab#10-M30W-S94M IgG
Map data
Sample
  • Complex: Complex of spike protein of SARS-CoV-2 Omicron BA.4 with Ab#10-M30W-S94M IgG.
    • Complex: Spike protein of SARS-CoV-2 Omicron BA.4 variant
    • Complex: Ab#10-M30W-S94M IgG
KeywordsSARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDu J / Pallesen J
Funding support United States, 2 items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Res Sq / Year: 2026
Title: Structure-Guided Design of Therapeutic Antibodies Targeting SARS-CoV-2 Omicron Variants.
Authors: Jesper Pallesen / Jianqiu Du / Yuanhan Wu / Sukanya Ghosh / Kelly Bayruns / Roopak Sadeesh / David Weiner
Abstract: The ongoing evolution of SARS-CoV-2, particularly the emergence of Omicron subvariants, compromised the effectiveness of many therapeutic antibodies. In this study, we employed a structure-guided ...The ongoing evolution of SARS-CoV-2, particularly the emergence of Omicron subvariants, compromised the effectiveness of many therapeutic antibodies. In this study, we employed a structure-guided computational design strategy to systematically optimize the COV2-2196 antibody for improved neutralization of Omicron variants. Through iterative rounds of computational design and experimental validation, we identified key paratope mutations that restored and enhanced antibody binding and neutralization potency against resistant viral strains. Cryo-EM structural analysis revealed the molecular basis for these improvements, highlighting how targeted modifications can accommodate epitope changes introduced by viral evolution. Our approach demonstrates that effective antibody optimization can be achieved using accessible computational resources, providing a practical framework for rapid therapeutic development. These findings underscore the potential of structure-based design to address challenges posed by viral antigenic drift and support the development of broadly effective antibody therapeutics for emerging infectious diseases.
History
DepositionMay 28, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_77347.png

Downloads & links

-
Map

FileDownload / File: emd_77347.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 512 pix.
= 539.648 Å		1.05 Å/pix.
x 512 pix.
= 539.648 Å		1.05 Å/pix.
x 512 pix.
= 539.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.121
Minimum - Maximum-0.88532 - 1.2672985
Average (Standard dev.)0.000047520105 (±0.011841535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 539.648 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_77347_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_77347_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of spike protein of SARS-CoV-2 Omicron BA.4 with Ab#10-M3...

EntireName: Complex of spike protein of SARS-CoV-2 Omicron BA.4 with Ab#10-M30W-S94M IgG.
Components
  • Complex: Complex of spike protein of SARS-CoV-2 Omicron BA.4 with Ab#10-M30W-S94M IgG.
    • Complex: Spike protein of SARS-CoV-2 Omicron BA.4 variant
    • Complex: Ab#10-M30W-S94M IgG

-
Supramolecule #1: Complex of spike protein of SARS-CoV-2 Omicron BA.4 with Ab#10-M3...

SupramoleculeName: Complex of spike protein of SARS-CoV-2 Omicron BA.4 with Ab#10-M30W-S94M IgG.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron BA.4

-
Supramolecule #2: Spike protein of SARS-CoV-2 Omicron BA.4 variant

SupramoleculeName: Spike protein of SARS-CoV-2 Omicron BA.4 variant / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron BA.4

-
Supramolecule #3: Ab#10-M30W-S94M IgG

SupramoleculeName: Ab#10-M30W-S94M IgG / type: complex / ID: 3 / Parent: 1
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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 536554
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