[English] 日本語
Yorodumi
- EMDB-44667: CoV SARS-2 spike protein complexed by mEM with monoclonal antibod... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44667
TitleCoV SARS-2 spike protein complexed by mEM with monoclonal antibody TXG-0078 Fab
Map data3D refined map of SARS-2 spike with monoclonal antibody TXG-0078 Fab (C1 symmetry)
Sample
  • Complex: Coronavirus SARS-2 spike in complex with monoclonal antibody TXG-0078 by mEM
KeywordsCoV / spike / SARS-2 / monoclonal antibody / TXG-0078 / complex / microfluidics / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsSewall LM / Ward AB / Torrents de la Pena A
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136621 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Nat Biomed Eng / Year: 2025
Title: Rapid and High-Throughput Imaging of Immune Complexes Using Microfluidics and Single Particle Electron Microscopy
Authors: Sewall LM / de Paiva Froes Rocha R / Gibson G / Louie M / Xie Z / Bangaru S / Tran AS / Ozorowski G / Mohanty S / Beutler N / Burton DR / Shaw AC / Batista FD / Chocarro Ruiz B / Torrents de la Pena A / Ward AB
History
DepositionApr 30, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44667.png

Downloads & links

-
Map

FileDownload / File: emd_44667.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D refined map of SARS-2 spike with monoclonal antibody TXG-0078 Fab (C1 symmetry)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.018109888 - 0.077562064
Average (Standard dev.)0.00016969038 (±0.0029182844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 527.36 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: 3D refined half map 1 of SARS-2 spike...

Fileemd_44667_half_map_1.map
Annotation3D refined half map 1 of SARS-2 spike with monoclonal antibody TXG-0078 Fab (C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: 3D refined half map 2 of SARS-2 spike...

Fileemd_44667_half_map_2.map
Annotation3D refined half map 2 of SARS-2 spike with monoclonal antibody TXG-0078 Fab (C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Coronavirus SARS-2 spike in complex with monoclonal antibody TXG-...

EntireName: Coronavirus SARS-2 spike in complex with monoclonal antibody TXG-0078 by mEM
Components
  • Complex: Coronavirus SARS-2 spike in complex with monoclonal antibody TXG-0078 by mEM

-
Supramolecule #1: Coronavirus SARS-2 spike in complex with monoclonal antibody TXG-...

SupramoleculeName: Coronavirus SARS-2 spike in complex with monoclonal antibody TXG-0078 by mEM
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: 10 mM Tris, 150 mM NaCl
StainingType: NEGATIVE / Material: Uranyl Formate

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 56000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

-
Image processing

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

6ohw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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