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- EMDB-35426: Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in c... -

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Entry
Database: EMDB / ID: EMD-35426
TitleCryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in complex with white-tailed deer ACE2
Map data
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in complex with white-tailed deer ACE2
    • Protein or peptide: Spike glycoproteinSpike protein
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
Keywordscomplex / VIRAL PROTEIN / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / 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 / proteolysis / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / 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 ...Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / 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
Similarity search - Domain/homology
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Odocoileus virginianus (white-tailed deer)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsHan P / Meng YM / Qi JX
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32192452 China
CitationJournal: J Virol / Year: 2023
Title: Structural basis of white-tailed deer, , ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity.
Authors: Pu Han / Yumin Meng / Di Zhang / Zepeng Xu / Zhiyuan Li / Xiaoqian Pan / Zhennan Zhao / Linjie Li / Lingfeng Tang / Jianxun Qi / Kefang Liu / George F Gao /
Abstract: SARS-CoV-2 has been expanding its host range, among which the white-tailed deer (WTD), became the first wildlife species infected on a large scale and might serve as a host reservoir for variants of ...SARS-CoV-2 has been expanding its host range, among which the white-tailed deer (WTD), became the first wildlife species infected on a large scale and might serve as a host reservoir for variants of concern (VOCs) in case no longer circulating in humans. In this study, we comprehensively assessed the binding of the WTD angiotensin-converting enzyme 2 (ACE2) receptor to the spike (S) receptor-binding domains (RBDs) from the SARS-CoV-2 prototype (PT) strain and multiple variants. We found that WTD ACE2 could be broadly recognized by all of the tested RBDs. We further determined the complex structures of WTD ACE2 with PT, Omicron BA.1, and BA.4/5 S trimer. Detailed structural comparison revealed the important roles of RBD residues on 486, 498, and 501 sites for WTD ACE2 binding. This study deepens our understanding of the interspecies transmission mechanisms of SARS-CoV-2 and further addresses the importance of constant monitoring on SARS-CoV-2 infections in wild animals. IMPORTANCE Even if we manage to eliminate the virus among humans, it will still circulate among wildlife and continuously be transmitted back to humans. A recent study indicated that WTD may serve as reservoir for nearly extinct SARS-CoV-2 strains. Therefore, it is critical to evaluate the binding abilities of SARS-CoV-2 variants to the WTD ACE2 receptor and elucidate the molecular mechanisms of binding of the RBDs to assess the risk of spillback events.
History
DepositionFeb 20, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35426.png

Downloads & links

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Map

FileDownload / File: emd_35426.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.3632318 - 1.4122244
Average (Standard dev.)-0.00051833654 (±0.02668336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 457.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35426_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35426_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in c...

EntireName: Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in complex with white-tailed deer ACE2
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in complex with white-tailed deer ACE2
    • Protein or peptide: Spike glycoproteinSpike protein
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in c...

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in complex with white-tailed deer ACE2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 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: 125.148039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QCVNLITRTQ SYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH AISGTNGTKR FDNPVLPFND GVYFASTEKS NIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDVYYHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKQGNF ...String:
QCVNLITRTQ SYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH AISGTNGTKR FDNPVLPFND GVYFASTEKS NIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDVYYHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKQGNF KNLREFVFKN IDGYFKIYSK HTPINLGRDL PQGFSALEPL VDLPIGINIT RFQTLLALHR SYLTPGDSSS GW TAGAAAY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKS FTVEKGIYQT SNFRVQPTES IVRFPNITNL CPF DEVFNA TRFASVYAWN RKRISNCVAD YSVLYNFAPF FAFKCYGVSP TKLNDLCFTN VYADSFVIRG NEVSQIAPGQ TGNI ADYNY KLPDDFTGCV IAWNSNKLDS KVGGNYNYRY RLFRKSNLKP FERDISTEIY QAGNKPCNGV AGVNCYFPLQ SYGFR PTYG VGHQPYRVVV LSFELLHAPA TVCGPKKSTN LVKNKCVNFN FNGLTGTGVL TESNKKFLPF QQFGRDIADT TDAVRD PQT LEILDITPCS FGGVSVITPG TNTSNQVAVL YQGVNCTEVP VAIHADQLTP TWRVYSTGSN VFQTRAGCLI GAEYVNN SY ECDIPIGAGI CASYQTQTKS HRRARSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDC T MYICGDSTEC SNLLLQYGSF CTQLKRALTG IAVEQDKNTQ EVFAQVKQIY KTPPIKYFGG FNFSQILPDP SKPSKRSPI EDLLFNKVTL ADAGFIKQYG DCLGDIAARD LICAQKFNGL TVLPPLLTDE MIAQYTSALL AGTITSGWTF GAGPALQIPF PMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTPSALGK LQDVVNHNAQ ALNTLVKQLS SKFGAISSVL N DILSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQSA PH GVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDVVIGIVNN TVY DPLQPE L

UniProtKB: Spike glycoprotein

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Macromolecule #2: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Odocoileus virginianus (white-tailed deer)
Molecular weightTheoretical: 76.530477 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STTEEQAKTF LEKFNHEAED LSYQSSLASW NYNTNITDEN VQKMNEARAK WSAFYEEQSR MAKTYSLEEI QNLTLKRQLK ALQQSGTSV LSAEKSKRLN TILNTMSTIY STGKVLDPNT QECLALEPGL DDIMENSRDY NRRLWAWEGW RAEVGKQLRP L YEEYVVLE ...String:
STTEEQAKTF LEKFNHEAED LSYQSSLASW NYNTNITDEN VQKMNEARAK WSAFYEEQSR MAKTYSLEEI QNLTLKRQLK ALQQSGTSV LSAEKSKRLN TILNTMSTIY STGKVLDPNT QECLALEPGL DDIMENSRDY NRRLWAWEGW RAEVGKQLRP L YEEYVVLE NEMARANNYE DYGDYWRGDY EVTEAGDYDY SRDQLMKDVE NTFAEIKPLY EQLHAYVRAK LMDTYPSYIS PT GCLPAHL LGDMWGRFWT NLYSLTVPFK HKPSIDVTEK MKNQSWDAER IFKEAEKFFV SISLPHMTQG FWDNSMLTEP GDG RKVVCH PTAWDLGKGD FRIKMCTKVT MDDFLTAHHE MGHIQYDMAY AAQPYLLRDG ANEGFHEAVG EIMSLSAATP HYLK ALGLL EPDFYEDNET EINFLLKQAL TIVGTLPFTY MLEKWRWMVF KGEIPKEQWM EKWWEMKREI VGVVEPLPHD ETYCD PACL FHVAEDYSFI RYYTRTIYQF QFHEALCKTA NHEGALFKCD ISNSTEAGQR LLQMLSLGKS EPWTLALESI VGIKTM DVK PLLNYFEPLF TWLKEQNRNS FVGWSTEWTP YSDQSIKVRI SLKSALGKNA DANCPFVWCV PPVSHLVAIV IRSAVTV SQ CCVQATLVLL NPGPKVPEE

UniProtKB: Angiotensin-converting enzyme

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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: 25 / 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: 2 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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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

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 294102
FSC plot (resolution estimation)

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