[English] 日本語
Yorodumi
- EMDB-34217: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34217
TitleCryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with rat ACE2 (local refinement)
Map data
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with mouse ACE2 (local refinement)
    • Complex: Rat angiotensin-converting enzyme 2
      • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Complex: Omicron BA.2 RBD
      • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / Omicron BA.2 / spike protein / VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of cardiac conduction ...Metabolism of Angiotensinogen to Angiotensins / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / metallocarboxypeptidase activity / negative regulation of signaling receptor activity / carboxypeptidase activity / positive regulation of cardiac muscle contraction / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / brush border membrane / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / virus receptor activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / endopeptidase activity / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / proteolysis / extracellular space / extracellular region / membrane / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Trp-Asp (WD) repeats signature.
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsZhao ZN / Xie YF / Chai Y / Qi JX / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants.
Authors: Zhennan Zhao / Yufeng Xie / Bin Bai / Chunliang Luo / Jingya Zhou / Weiwei Li / Yumin Meng / Linjie Li / Dedong Li / Xiaomei Li / Xiaoxiong Li / Xiaoyun Wang / Junqing Sun / Zepeng Xu / ...Authors: Zhennan Zhao / Yufeng Xie / Bin Bai / Chunliang Luo / Jingya Zhou / Weiwei Li / Yumin Meng / Linjie Li / Dedong Li / Xiaomei Li / Xiaoxiong Li / Xiaoyun Wang / Junqing Sun / Zepeng Xu / Yeping Sun / Wei Zhang / Zheng Fan / Xin Zhao / Linhuan Wu / Juncai Ma / Odel Y Li / Guijun Shang / Yan Chai / Kefang Liu / Peiyi Wang / George F Gao / Jianxun Qi /
Abstract: Multiple SARS-CoV-2 Omicron sub-variants, such as BA.2, BA.2.12.1, BA.4, and BA.5, emerge one after another. BA.5 has become the dominant strain worldwide. Additionally, BA.2.75 is significantly ...Multiple SARS-CoV-2 Omicron sub-variants, such as BA.2, BA.2.12.1, BA.4, and BA.5, emerge one after another. BA.5 has become the dominant strain worldwide. Additionally, BA.2.75 is significantly increasing in some countries. Exploring their receptor binding and interspecies transmission risk is urgently needed. Herein, we examine the binding capacities of human and other 28 animal ACE2 orthologs covering nine orders towards S proteins of these sub-variants. The binding affinities between hACE2 and these sub-variants remain in the range as that of previous variants of concerns (VOCs) or interests (VOIs). Notably, R493Q reverse mutation enhances the bindings towards ACE2s from humans and many animals closely related to human life, suggesting an increased risk of cross-species transmission. Structures of S/hACE2 or RBD/hACE2 complexes for these sub-variants and BA.2 S binding to ACE2 of mouse, rat or golden hamster are determined to reveal the molecular basis for receptor binding and broader interspecies recognition.
History
DepositionSep 3, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateAug 2, 2023-
Current statusAug 2, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34217.png

Downloads & links

-
Map

FileDownload / File: emd_34217.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.0017622093 - 1.9441984
Average (Standard dev.)0.0002051998 (±0.011209786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 450.56 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_34217_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_34217_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with ...

EntireName: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with mouse ACE2 (local refinement)
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with mouse ACE2 (local refinement)
    • Complex: Rat angiotensin-converting enzyme 2
      • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Complex: Omicron BA.2 RBD
      • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with ...

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with mouse ACE2 (local refinement)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)

-
Supramolecule #2: Rat angiotensin-converting enzyme 2

SupramoleculeName: Rat angiotensin-converting enzyme 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

-
Supramolecule #3: Omicron BA.2 RBD

SupramoleculeName: Omicron BA.2 RBD / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

-
Macromolecule #1: Processed angiotensin-converting enzyme 2

MacromoleculeName: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 69.197625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SLIEEKAESF LNKFNQEAED LSYQSSLASW NYNTNITEEN AQKMNEAAAK WSAFYEEQSK IAQNFSLQEI QNATIKRQLK ALQQSGSSA LSPDKNKQLN TILNTMSTIY STGKVCNSMN PQECFLLEPG LDEIMATSTD YNRRLWAWEG WRAEVGKQLR P LYEEYVVL ...String:
SLIEEKAESF LNKFNQEAED LSYQSSLASW NYNTNITEEN AQKMNEAAAK WSAFYEEQSK IAQNFSLQEI QNATIKRQLK ALQQSGSSA LSPDKNKQLN TILNTMSTIY STGKVCNSMN PQECFLLEPG LDEIMATSTD YNRRLWAWEG WRAEVGKQLR P LYEEYVVL KNEMARANNY EDYGDYWRGD YEAEGVEGYN YNRNQLIEDV ENTFKEIKPL YEQLHAYVRT KLMEVYPSYI SP TGCLPAH LLGDMWGRFW TNLYPLTTPF LQKPNIDVTD AMVNQSWDAE RIFKEAEKFF VSVGLPQMTP GFWTNSMLTE PGD DRKVVC HPTAWDLGHG DFRIKMCTKV TMDNFLTAHH EMGHIQYDMA YAKQPFLLRN GANEGFHEAV GEIMSLSAAT PKHL KSIGL LPSNFQEDNE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FQDKIPREQW TKKWWEMKRE IVGVVEPLPH DETYC DPAS LFHVSNDYSF IRYYTRTIYQ FQFQEALCQA AKHDGPLHKC DISNSTEAGQ KLLNMLSLGN SGPWTLALEN VVGSRN MDV KPLLNYFQPL FVWLKEQNRN STVGWSTDWS PYAD

UniProtKB: Angiotensin-converting enzyme 2

-
Macromolecule #2: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 2 / Details: Omicron BA.2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.039873 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TNLCPFDEVF NATRFASVYA WNRKRISNCV ADYSVLYNFA PFFAFKCYGV SPTKLNDLCF TNVYADSFVI RGNEVSQIAP GQTGNIADY NYKLPDDFTG CVIAWNSNKL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGNKPCN GVAGFNCYFP L RSYGFRPT ...String:
TNLCPFDEVF NATRFASVYA WNRKRISNCV ADYSVLYNFA PFFAFKCYGV SPTKLNDLCF TNVYADSFVI RGNEVSQIAP GQTGNIADY NYKLPDDFTG CVIAWNSNKL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGNKPCN GVAGFNCYFP L RSYGFRPT YGVGHQPYRV VVLSFELLHA PATVCGP

UniProtKB: Spike glycoprotein

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

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

7knb

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50491

+
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