[English] 日本語
Yorodumi
- EMDB-46715: MERS NTD-specific polyclonal antibodies -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46715
TitleMERS NTD-specific polyclonal antibodies
Map dataEM map
Sample
  • Complex: MERS spike protein complexed with RBD-depleted polyclonal Fabs from MERS-vaccinated mice sera
Keywordsspike / MERS / polyclonal antibody / NTD complex / VIRAL PROTEIN
Biological speciesMiddle East respiratory syndrome-related coronavirus
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsWard AB / Bangaru S
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: iScience / Year: 2025
Title: MERS-CoV spike vaccine-induced N-terminal domain-specific antibodies are more protective than receptor binding domain-specific antibodies.
Authors: Olubukola M Abiona / Nianshuang Wang / Sarah R Leist / Alexandra Schäfer / Adam S Cockrell / Lingshu Wang / Sandhya Bangaru / Laura Stevens / Rachel L Graham / Jacob F Kocher / Yaroslav ...Authors: Olubukola M Abiona / Nianshuang Wang / Sarah R Leist / Alexandra Schäfer / Adam S Cockrell / Lingshu Wang / Sandhya Bangaru / Laura Stevens / Rachel L Graham / Jacob F Kocher / Yaroslav Tsybovsky / Masaru Kanekiyo / Azad Kumar / Kaitlyn M Morabito / Osnat Rosen / Wei Shi / Anne Werner / Yi Zhang / Cynthia Ziwawo / Christian K O Dzuvor / Charis Palandjian / Connor Eastman / Hannah R Matthews / Jeswin Joseph / James D Chappell / Wing-Pui Kong / John R Mascola / Andrew B Ward / Mark R Denison / Ralph Baric / Jason S McLellan / Barney S Graham / Kizzmekia S Corbett-Helaire /
Abstract: The COVID-19 pandemic underscores the need to prepare for future emerging coronavriuses (CoVs) by understanding the principles behind effective CoV vaccine design such as protective immunity and ...The COVID-19 pandemic underscores the need to prepare for future emerging coronavriuses (CoVs) by understanding the principles behind effective CoV vaccine design such as protective immunity and antibody responses. To study which epitopes and subdomains contribute to protection, we utilized the prefusion-stabilized spike protein of MERS-CoV, MERS S-2P, as a vaccine immunogen. Vaccination with MERS S-2P elicited both receptor-binding domain (RBD)- and non-RBD-specific antibodies, including N-terminal domain (NTD)-specific G2-and CDC2-A2-like antibodies. Intriguingly, the immunogen MERS S-2P_ΔRBD, MERS S-2P with the RBDs removed, protects comparably to S1 and S-2P immunogens against MERS-CoV challenge. Moreover, passive transfer studies of polyclonal IgG from MERS S-2P immunized mice depleted of subdomain-specific antibodies demonstrated that non-RBD antibodies protected more than non-NTD antibodies. Altogether, these findings illustrate that protection is not solely driven by RBD-specific antibodies and highlights the importance of targeting non-RBD sites in future CoV vaccine designs.
History
DepositionAug 23, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46715.png

Downloads & links

-
Map

FileDownload / File: emd_46715.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 256 pix.
= 524.8 Å		2.05 Å/pix.
x 256 pix.
= 524.8 Å		2.05 Å/pix.
x 256 pix.
= 524.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.03812811 - 0.104234196
Average (Standard dev.)-0.000005818567 (±0.0038975643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 524.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map 1

Fileemd_46715_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_46715_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MERS spike protein complexed with RBD-depleted polyclonal Fabs fr...

EntireName: MERS spike protein complexed with RBD-depleted polyclonal Fabs from MERS-vaccinated mice sera
Components
  • Complex: MERS spike protein complexed with RBD-depleted polyclonal Fabs from MERS-vaccinated mice sera

-
Supramolecule #1: MERS spike protein complexed with RBD-depleted polyclonal Fabs fr...

SupramoleculeName: MERS spike protein complexed with RBD-depleted polyclonal Fabs from MERS-vaccinated mice sera
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate
GridModel: EMS Lacey Carbon / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 6.3 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 56000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 3560
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION

+
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