[English] 日本語
Yorodumi
- EMDB-32727: Cryo-EM structure of SARS-CoV-2 Omicron spike receptor-binding do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32727
TitleCryo-EM structure of SARS-CoV-2 Omicron spike receptor-binding domain in complex with mouse ACE2
Map data
Sample
  • Complex: Complex of SARS-CoV-2 Omicron spike protein with mouse ACE2
    • Complex: mouse ACE2
      • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Complex: SARS-CoV-2 Omicron spike protein
      • Protein or peptide: Spike glycoprotein
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplex / Viral protein
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy ...Metabolism of Angiotensinogen to Angiotensins / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / carboxypeptidase activity / angiotensin maturation / metallocarboxypeptidase activity / positive regulation of cardiac muscle contraction / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / virus receptor activity / endopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / cilium / symbiont-mediated suppression of host innate immune response / apical plasma membrane / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular region / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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 / Coronavirus spike glycoprotein S1, C-terminal ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Trp-Asp (WD) repeats signature.
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsHan P / Xie Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32192452 China
CitationJournal: Cell Discov / Year: 2022
Title: Broader-species receptor binding and structural bases of Omicron SARS-CoV-2 to both mouse and palm-civet ACE2s.
Authors: Linjie Li / Pu Han / Baihan Huang / Yufeng Xie / Weiwei Li / Di Zhang / Pengcheng Han / Zepeng Xu / Bin Bai / Jingya Zhou / Xinrui Kang / Xiaomei Li / Anqi Zheng / Rong Zhang / Shitong Qiao ...Authors: Linjie Li / Pu Han / Baihan Huang / Yufeng Xie / Weiwei Li / Di Zhang / Pengcheng Han / Zepeng Xu / Bin Bai / Jingya Zhou / Xinrui Kang / Xiaomei Li / Anqi Zheng / Rong Zhang / Shitong Qiao / Xin Zhao / Jianxun Qi / Qihui Wang / Kefang Liu / George Fu Gao /
Abstract: The Omicron variant of SARS-CoV-2 carries multiple unusual mutations, particularly in the receptor-binding domain (RBD) of the spike (S) protein. Moreover, host-adapting mutations, such as residues ...The Omicron variant of SARS-CoV-2 carries multiple unusual mutations, particularly in the receptor-binding domain (RBD) of the spike (S) protein. Moreover, host-adapting mutations, such as residues 493, 498, and 501, were also observed in the Omicron RBD, which indicates that it is necessary to evaluate the interspecies transmission risk of the Omicron variant. Herein, we evaluated the interspecies recognition of the Omicron BA.1 and Delta RBDs by 27 ACE2 orthologs, including humans. We found that Omicron BA.1 expanded its receptor binding spectra to palm-civet, rodents, more bats (least horseshoe bat and greater horseshoe bat) and lesser hedgehog tenrec. Additionally, we determined the cryo-electron microscopy (cryo-EM) structure of the Omicron BA.1 S protein complexed with mouse ACE2 (mACE2) and the crystal structure of Omicron RBD complexed with palm-civet ACE2 (cvACE2). Several key residues for the host range have been identified. These results suggest that surveillance should be enhanced on the Omicron variant for its broader-species receptor binding to prevent spillover and expansion of reservoir hosts for a prolonged pandemic.
History
DepositionJan 26, 2022-
Header (metadata) releaseJun 8, 2022-
Map releaseJun 8, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32727.png

Downloads & links

-
Map

FileDownload / File: emd_32727.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.689
Minimum - Maximum-2.9215314 - 4.766083
Average (Standard dev.)0.00039035024 (±0.057861477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Complex of SARS-CoV-2 Omicron spike protein with mouse ACE2

EntireName: Complex of SARS-CoV-2 Omicron spike protein with mouse ACE2
Components
  • Complex: Complex of SARS-CoV-2 Omicron spike protein with mouse ACE2
    • Complex: mouse ACE2
      • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Complex: SARS-CoV-2 Omicron spike protein
      • Protein or peptide: Spike glycoprotein
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Complex of SARS-CoV-2 Omicron spike protein with mouse ACE2

SupramoleculeName: Complex of SARS-CoV-2 Omicron spike protein with mouse ACE2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #2: mouse ACE2

SupramoleculeName: mouse ACE2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

-
Supramolecule #3: SARS-CoV-2 Omicron spike protein

SupramoleculeName: SARS-CoV-2 Omicron spike protein / 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 / EC number: angiotensin-converting enzyme 2
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 69.218594 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QSLTEENAKT FLNNFNQEAE DLSYQSSLAS WNYNTNITEE NAQKMSEAAA KWSAFYEEQS KTAQSFSLQE IQTPIIKRQL QALQQSGSS ALSADKNKQL NTILNTMSTI YSTGKVCNPK NPQECLLLEP GLDEIMATST DYNSRLWAWE GWRAEVGKQL R PLYEEYVV ...String:
QSLTEENAKT FLNNFNQEAE DLSYQSSLAS WNYNTNITEE NAQKMSEAAA KWSAFYEEQS KTAQSFSLQE IQTPIIKRQL QALQQSGSS ALSADKNKQL NTILNTMSTI YSTGKVCNPK NPQECLLLEP GLDEIMATST DYNSRLWAWE GWRAEVGKQL R PLYEEYVV LKNEMARANN YNDYGDYWRG DYEAEGADGY NYNRNQLIED VERTFAEIKP LYEHLHAYVR RKLMDTYPSY IS PTGCLPA HLLGDMWGRF WTNLYPLTVP FAQKPNIDVT DAMMNQGWDA ERIFQEAEKF FVSVGLPHMT QGFWANSMLT EPA DGRKVV CHPTAWDLGH GDFRIKMCTK VTMDNFLTAH HEMGHIQYDM AYARQPFLLR NGANEGFHEA VGEIMSLSAA TPKH LKSIG LLPSDFQEDS ETEINFLLKQ ALTIVGTLPF TYMLEKWRWM VFRGEIPKEQ WMKKWWEMKR EIVGVVEPLP HDETY CDPA SLFHVSNDYS FIRYYTRTIY QFQFQEALCQ AAKYNGSLHK CDISNSTEAG QKLLKMLSLG NSEPWTKALE NVVGAR NMD VKPLLNYFQP LFDWLKEQNR NSFVGWNTEW SPYAD

UniProtKB: Angiotensin-converting enzyme 2

-
Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 137.201359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISGTNG TKRFDNPVLP FNDGVYFASI EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKQGNF ...String:
QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISGTNG TKRFDNPVLP FNDGVYFASI EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKQGNF KNLREFVFKN IDGYFKIYSK HTPIIVRDEP ELPQGFSALE PLVDLPIGIN ITRFQTLLAL HRSYLTPGDS SS GWTAGAA AYYVGYLQPR TFLLKYNENG TITDAVDCAL DPLSETKCTL KSFTVEKGIY QTSNFRVQPT ESIVRFPNIT NLC PFDEVF NATRFASVYA WNRKRISNCV ADYSVLYNLA PFFTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTG NIADY NYKLPDDFTG CVIAWNSNKL DSKVSGNYNY LYRLFRKSNL KPFERDISTE IYQAGNKPCN GVAGFNCYFP LRSYS FRPT YGVGHQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLKGTG VLTESNKKFL PFQQFGRDIA DTTDAV RDP QTLEILDITP CSFGGVSVIT PGTNTSNQVA VLYQGVNCTE VPVAIHADQL TPTWRVYSTG SNVFQTRAGC LIGAEYV NN SYECDIPIGA GICASYQTQT KSHRRARSVA SQSIIAYTMS LGAENSVAYS NNSIAIPTNF TISVTTEILP VSMTKTSV D CTMYICGDST ECSNLLLQYG SFCTQLKRAL TGIAVEQDKN TQEVFAQVKQ IYKTPPIKYF GGFNFSQILP DPSKPSKRS PIEDLLFNKV TLADAGFIKQ YGDCLGDIAA RDLICAQKFK GLTVLPPLLT DEMIAQYTSA LLAGTITSGW TFGAGPALQI PFPMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLSSTPSAL GKLQDVVNHN AQALNTLVKQ LSSKFGAISS V LNDIFSRL DPPEAEVQID RLITGRLQSL QTYVTQQLIR AAEIRASANL AATKMSECVL GQSKRVDFCG KGYHLMSFPQ SA PHGVVFL HVTYVPAQEK NFTTAPAICH DGKAHFPREG VFVSNGTHWF VTQRNFYEPQ IITTDNTFVS GNCDVVIGIV NNT VYDPLQ PELDSFKEEL DKYFKNHTSP DVDLGDISGI NASVVNIQKE IDRLNEVAKN LNESLIDLQE LGKYEQGSGY IPEA PRDGQ AYVRKDGEWV LLSTFLGSAW SHPQFEK

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 503967
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6lzg


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7wri:
Cryo-EM structure of SARS-CoV-2 Omicron spike receptor-binding domain in complex with mouse ACE2

+
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