[English] 日本語
Yorodumi
- EMDB-25011: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25011
TitleSpike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1988
Map data3D refined map of HKU1 spike with donor 1988 polyclonal Fabs (C1 symmetry)
Sample
  • Complex: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1988
Biological speciesHuman coronavirus OC43
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsWard AB / Bangaru S / Sewall LM / Jackson AM
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: Sci Adv / Year: 2022
Title: Structural mapping of antibody landscapes to human betacoronavirus spike proteins.
Authors: Bangaru S / Antanasijevic A / Kose N / Sewall LM / Jackson AM / Suryadevara N / Zhan X / Torres JL / Copps J / de la Pena AT / Crowe Jr JE / Ward AB
History
DepositionSep 27, 2021-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateMay 18, 2022-
Current statusMay 18, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_25011.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D refined map of HKU1 spike with donor 1988 polyclonal Fabs (C1 symmetry)
Voxel sizeX=Y=Z: 2.06 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.037389584 - 0.087013654
Average (Standard dev.)0.00017632663 (±0.004240211)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 412.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs compl...

EntireName: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1988
Components
  • Complex: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1988

-
Supramolecule #1: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs compl...

SupramoleculeName: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1988
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human coronavirus OC43
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F cells

-
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
GridMaterial: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE

-
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: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 100000
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