[English] 日本語
Yorodumi
- EMDB-47588: Negative stain EM map of polyclonal serum from mouse immunized wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47588
TitleNegative stain EM map of polyclonal serum from mouse immunized with MERS-CoV RBD-I53-50 in complex with MERS S-2P
Map dataNegative stain EM map of polyclonal serum from mouse immunized with MERS-CoV RBD-I53-50 in complex with MERS S-2P.
Sample
  • Complex: Immune complex 1 of prefusion MERS-CoV spike glycoprotein stabilized with 2P mutations with polyclonal Fabs from mice immunized with MERS-CoV RBD-I53-50.
KeywordsFab / serum / immune complex / MERS-S2P / VIRAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
AuthorsChao CW / King NP
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI167966 United States
National Science Foundation (NSF, United States)DGE-2140004 United States
CitationJournal: Cell Rep / Year: 2024
Title: Protein nanoparticle vaccines induce potent neutralizing antibody responses against MERS-CoV.
Authors: Cara W Chao / Kaitlin R Sprouse / Marcos C Miranda / Nicholas J Catanzaro / Miranda L Hubbard / Amin Addetia / Cameron Stewart / Jack T Brown / Annie Dosey / Adian Valdez / Rashmi ...Authors: Cara W Chao / Kaitlin R Sprouse / Marcos C Miranda / Nicholas J Catanzaro / Miranda L Hubbard / Amin Addetia / Cameron Stewart / Jack T Brown / Annie Dosey / Adian Valdez / Rashmi Ravichandran / Grace G Hendricks / Maggie Ahlrichs / Craig Dobbins / Alexis Hand / Jackson McGowan / Boston Simmons / Catherine Treichel / Isabelle Willoughby / Alexandra C Walls / Andrew T McGuire / Elizabeth M Leaf / Ralph S Baric / Alexandra Schäfer / David Veesler / Neil P King /
Abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a betacoronavirus that causes severe respiratory illness in humans. There are no licensed vaccines against MERS-CoV and only a few ...Middle East respiratory syndrome coronavirus (MERS-CoV) is a betacoronavirus that causes severe respiratory illness in humans. There are no licensed vaccines against MERS-CoV and only a few candidates in phase I clinical trials. Here, we develop MERS-CoV vaccines utilizing a computationally designed protein nanoparticle platform that has generated safe and immunogenic vaccines against various enveloped viruses, including a licensed vaccine for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Two-component nanoparticles displaying spike (S)-derived antigens induce neutralizing responses and protect mice against challenge with mouse-adapted MERS-CoV. Epitope mapping reveals the dominant responses elicited by immunogens displaying the prefusion-stabilized S-2P trimer, receptor binding domain (RBD), or N-terminal domain (NTD). An RBD nanoparticle elicits antibodies targeting multiple non-overlapping epitopes in the RBD. Our findings demonstrate the potential of two-component nanoparticle vaccine candidates for MERS-CoV and suggest that this platform technology could be broadly applicable to betacoronavirus vaccine development.
History
DepositionOct 31, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47588.png

Downloads & links

-
Map

FileDownload / File: emd_47588.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of polyclonal serum from mouse immunized with MERS-CoV RBD-I53-50 in complex with MERS S-2P.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.49 Å/pix.
x 260 pix.
= 647.4 Å		2.49 Å/pix.
x 260 pix.
= 647.4 Å		2.49 Å/pix.
x 260 pix.
= 647.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.49 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.13
Minimum - Maximum-1.7825919 - 4.828818
Average (Standard dev.)-0.017886698 (±0.17028254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 647.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Negative stain EM map of polyclonal serum from...

Fileemd_47588_half_map_1.map
AnnotationNegative stain EM map of polyclonal serum from mouse immunized with MERS-CoV RBD-I53-50 in complex with MERS S-2P.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Negative stain EM map of polyclonal serum from...

Fileemd_47588_half_map_2.map
AnnotationNegative stain EM map of polyclonal serum from mouse immunized with MERS-CoV RBD-I53-50 in complex with MERS S-2P.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Immune complex 1 of prefusion MERS-CoV spike glycoprotein stabili...

EntireName: Immune complex 1 of prefusion MERS-CoV spike glycoprotein stabilized with 2P mutations with polyclonal Fabs from mice immunized with MERS-CoV RBD-I53-50.
Components
  • Complex: Immune complex 1 of prefusion MERS-CoV spike glycoprotein stabilized with 2P mutations with polyclonal Fabs from mice immunized with MERS-CoV RBD-I53-50.

-
Supramolecule #1: Immune complex 1 of prefusion MERS-CoV spike glycoprotein stabili...

SupramoleculeName: Immune complex 1 of prefusion MERS-CoV spike glycoprotein stabilized with 2P mutations with polyclonal Fabs from mice immunized with MERS-CoV RBD-I53-50.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: Uranyl formate

-
Electron microscopy

MicroscopeTFS TALOS L120C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos L120C / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE / Details: Ab Initio model generation
Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2478
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC

+
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