[English] 日本語
Yorodumi
- EMDB-15586: BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (two up, full) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15586
TitleBA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (two up, full)
Map data42
Sample
  • Complex: BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2
    • Complex: BA.4/5 SARS-CoV-2 Spike
    • Complex: Mouse ACE2
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsLau K / Ni D / Beckert B / Nazarov S / Myasnikov A / Pojer F / Stahlberg H / Uchikawa E
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationNCCR transcure Switzerland
Citation
Journal: Plos Pathog. / Year: 2023
Title: Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range
Authors: Ni D / Turelli P / Beckert B / Nazarov S / Uchikawa E / Myasnikov A / Pojer F / Trono D / Stahlberg H / Lau K
#1: Journal: Biorxiv / Year: 2023
Title: Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range
Authors: Ni D / Turelli P / Beckert B / Nazarov S / Uchikawa E / Myasnikov A / Pojer F / Trono D / Stahlberg H / Lau K
History
DepositionAug 13, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 15, 2023-
Current statusMar 15, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15586.png

Downloads & links

-
Map

FileDownload / File: emd_15586.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation42
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 360 pix.
= 365.184 Å		1.01 Å/pix.
x 360 pix.
= 365.184 Å		1.01 Å/pix.
x 360 pix.
= 365.184 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0144 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0775
Minimum - Maximum-0.49717668 - 0.8812032
Average (Standard dev.)-0.0005975383 (±0.019581782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 365.184 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: 42

Fileemd_15586_half_map_1.map
Annotation42
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: 42

Fileemd_15586_half_map_2.map
Annotation42
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2

EntireName: BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2
Components
  • Complex: BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2
    • Complex: BA.4/5 SARS-CoV-2 Spike
    • Complex: Mouse ACE2

-
Supramolecule #1: BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2

SupramoleculeName: BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Molecular weightTheoretical: 430 KDa

-
Supramolecule #2: BA.4/5 SARS-CoV-2 Spike

SupramoleculeName: BA.4/5 SARS-CoV-2 Spike / type: complex / ID: 2 / Chimera: Yes / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

-
Supramolecule #3: Mouse ACE2

SupramoleculeName: Mouse ACE2 / type: complex / ID: 3 / Chimera: Yes / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE
DetailsBA.4/5 SARS-CoV-2 Spike bound to mouse ACE2

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94718
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
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