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- EMDB-32726: Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in com... -

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Basic information

Entry
Database: EMDB / ID: EMD-32726
TitleCryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with mouse ACE2
Map data
Sample
  • Complex: Complex of SARS-CoV-2 Omicron BA.1 spike protein with mouse ACE2
    • Complex: SARS-CoV-2 Omicron BA.1 spike protein
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: mouse ACE2Angiotensin-converting enzyme 2
      • Protein or peptide: Processed angiotensin-converting enzyme 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / 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 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 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / carboxypeptidase activity / positive regulation of cardiac muscle contraction / brush border membrane / negative regulation of smooth muscle cell proliferation / 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 / endopeptidase activity / host cell surface / host extracellular space / 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 / apical plasma membrane / 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 / proteolysis / extracellular space / 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 speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsHan P / Xie Y / Qi J
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) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32726.png

Downloads & links

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Map

FileDownload / File: emd_32726.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.489
Minimum - Maximum-3.6916893 - 6.444451
Average (Standard dev.)0.00027681244 (±0.087451)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Sample components

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Entire : Complex of SARS-CoV-2 Omicron BA.1 spike protein with mouse ACE2

EntireName: Complex of SARS-CoV-2 Omicron BA.1 spike protein with mouse ACE2
Components
  • Complex: Complex of SARS-CoV-2 Omicron BA.1 spike protein with mouse ACE2
    • Complex: SARS-CoV-2 Omicron BA.1 spike protein
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: mouse ACE2Angiotensin-converting enzyme 2
      • Protein or peptide: Processed angiotensin-converting enzyme 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

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

SupramoleculeName: Complex of SARS-CoV-2 Omicron BA.1 spike protein with mouse ACE2
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: SARS-CoV-2 Omicron BA.1 spike protein

SupramoleculeName: SARS-CoV-2 Omicron BA.1 spike protein / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: mouse ACE2

SupramoleculeName: mouse ACE2 / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 138.041594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPRGPVAALL LLILHGAWSC VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HVISGTNGTK RFDNPVLPF NDGVYFASIE KSNIIRGWIF GTTLDSKTQS LLIVNNATNV VIKVCEFQFC NDPFLDHKNN KSWMESEFRV Y SSANNCTF ...String:
MPRGPVAALL LLILHGAWSC VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HVISGTNGTK RFDNPVLPF NDGVYFASIE KSNIIRGWIF GTTLDSKTQS LLIVNNATNV VIKVCEFQFC NDPFLDHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PIIVREPEDL PQGFSALEPL VDLPIGINIT RF QTLLALH RSYLTPGDSS SGWTAGAAAY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKS FTVEKGIYQT SNF RVQPTE SIVRFPNITN LCPFDEVFNA TRFASVYAWN RKRISNCVAD YSVLYNLAPF FTFKCYGVSP TKLNDLCFTN VYAD SFVIR GDEVRQIAPG QTGNIADYNY KLPDDFTGCV IAWNSNKLDS KVSGNYNYLY RLFRKSNLKP FERDISTEIY QAGNK PCNG VAGFNCYFPL RSYSFRPTYG VGHQPYRVVV LSFELLHAPA TVCGPKKSTN LVKNKCVNFN FNGLKGTGVL TESNKK FLP FQQFGRDIAD TTDAVRDPQT LEILDITPCS FGGVSVITPG TNTSNQVAVL YQGVNCTEVP VAIHADQLTP TWRVYST GS NVFQTRAGCL IGAEYVNNSY ECDIPIGAGI CASYQTQTKS HGSASSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNF T ISVTTEILPV SMTKTSVDCT MYICGDSTEC SNLLLQYGSF CTQLKRALTG IAVEQDKNTQ EVFAQVKQIY KTPPIKYFG GFNFSQILPD PSKPSKRSPI EDLLFNKVTL ADAGFIKQYG DCLGDIAARD LICAQKFKGL TVLPPLLTDE MIAQYTSALL AGTITSGWT FGAGPALQIP FPMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTPSALGK LQDVVNHNAQ A LNTLVKQL SSKFGAISSV LNDIFSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SK RVDFCGK GYHLMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTD NTFVSG NCDVVIGIVN NTVYDPLQPE LDSFKEELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLI DLQEL GKYEQLVPRG SGYIPEAPRD GQAYVRKDGE WVLLSTFL

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Macromolecule #2: Processed angiotensin-converting enzyme 2

MacromoleculeName: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 23 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.00 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 81000 / Illumination 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 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 503967
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7xd7

RefinementSpace: REAL
Output model

PDB-7wrh:
Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with mouse ACE2

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