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- EMDB-37711: Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 RBD in complex wi... -

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Entry
Database: EMDB / ID: EMD-37711
TitleCryo-EM structure of SARS-CoV-2 Omicron BA.2.86 RBD in complex with human ACE2
Map dataCryo-EM map of SARS-CoV-2 variant BA.2.86 RBD( receptor binding domain) in complex with hACE2( angiotensin converting enzyme 2)
Sample
  • Complex: Cryo-EM map of SARS-CoV-2 variant BA.2.86 RBD( receptor binding domain) in complex with hACE2( angiotensin converting enzyme 2)
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Processed angiotensin-converting enzyme 2
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / Omicron / BA.2.86 / RBD / human ACE2 / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / Attachment and Entry / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of transmembrane transporter activity / regulation of cytokine production / blood vessel diameter maintenance / brush border membrane / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / 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 / Potential therapeutics for SARS / 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 / membrane raft / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / symbiont 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 exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane
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
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: 2.89 Å
AuthorsLi LJ / Gu YH / Qi JX / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010202 China
CitationJournal: Structure / Year: 2024
Title: Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants.
Authors: Linjie Li / Kaiyuan Shi / Yuhang Gu / Zepeng Xu / Chang Shu / Dedong Li / Junqing Sun / Mengqing Cong / Xiaomei Li / Xin Zhao / Guanghui Yu / Songnian Hu / Hui Tan / Jianxun Qi / Xiaopeng Ma ...Authors: Linjie Li / Kaiyuan Shi / Yuhang Gu / Zepeng Xu / Chang Shu / Dedong Li / Junqing Sun / Mengqing Cong / Xiaomei Li / Xin Zhao / Guanghui Yu / Songnian Hu / Hui Tan / Jianxun Qi / Xiaopeng Ma / Kefang Liu / George F Gao /
Abstract: The recently emerged BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 variants have a growth advantage. In this study, we explore the structural bases of receptor binding and immune evasion for the Omicron BA.2. ...The recently emerged BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 variants have a growth advantage. In this study, we explore the structural bases of receptor binding and immune evasion for the Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Our findings reveal that BA.2.86 exhibits strong receptor binding, whereas its JN.1 sub-lineage displays a decreased binding affinity to human ACE2 (hACE2). Through complex structure analyses, we observed that the reversion of R493Q in BA.2.86 receptor binding domain (RBD) plays a facilitating role in receptor binding, while the L455S substitution in JN.1 RBD restores optimal affinity. Furthermore, the structure of monoclonal antibody (mAb) S309 complexed with BA.2.86 RBD highlights the importance of the K356T mutation, which brings a new N-glycosylation motif, altering the binding pattern of mAbs belonging to RBD-5 represented by S309. These findings emphasize the importance of closely monitoring BA.2.86 and its sub-lineages to prevent another wave of SARS-CoV-2 infections.
History
DepositionOct 9, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37711.png

Downloads & links

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Map

FileDownload / File: emd_37711.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of SARS-CoV-2 variant BA.2.86 RBD( receptor binding domain) in complex with hACE2( angiotensin converting enzyme 2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 320 pix.
= 220.8 Å		0.69 Å/pix.
x 320 pix.
= 220.8 Å		0.69 Å/pix.
x 320 pix.
= 220.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.0016833883 - 1.9510883
Average (Standard dev.)0.0013772107 (±0.027296131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 220.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-B map of SARS-CoV-2 variant BA.2.86 RBD( receptor...

Fileemd_37711_half_map_1.map
AnnotationHalf-B map of SARS-CoV-2 variant BA.2.86 RBD( receptor binding domain) in complex with hACE2( angiotensin converting enzyme 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-A map of SARS-CoV-2 variant BA.2.86 RBD( receptor...

Fileemd_37711_half_map_2.map
AnnotationHalf-A map of SARS-CoV-2 variant BA.2.86 RBD( receptor binding domain) in complex with hACE2( angiotensin converting enzyme 2)
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 map of SARS-CoV-2 variant BA.2.86 RBD( receptor binding d...

EntireName: Cryo-EM map of SARS-CoV-2 variant BA.2.86 RBD( receptor binding domain) in complex with hACE2( angiotensin converting enzyme 2)
Components
  • Complex: Cryo-EM map of SARS-CoV-2 variant BA.2.86 RBD( receptor binding domain) in complex with hACE2( angiotensin converting enzyme 2)
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Processed angiotensin-converting enzyme 2
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM map of SARS-CoV-2 variant BA.2.86 RBD( receptor binding d...

SupramoleculeName: Cryo-EM map of SARS-CoV-2 variant BA.2.86 RBD( receptor binding domain) in complex with hACE2( angiotensin converting enzyme 2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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: Homo sapiens (human)
Molecular weightTheoretical: 70.386992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSTIEEQAKT FLDKFNHEAE DLFYQSSLAS WNYNTNITEE NVQNMNNAGD KWSAFLKEQS TLAQMYPLQE IQNLTVKLQL QALQQNGSS VLSEDKSKRL NTILNTMSTI YSTGKVCNPD NPQECLLLEP GLNEIMANSL DYNERLWAWE SWRSEVGKQL R PLYEEYVV ...String:
QSTIEEQAKT FLDKFNHEAE DLFYQSSLAS WNYNTNITEE NVQNMNNAGD KWSAFLKEQS TLAQMYPLQE IQNLTVKLQL QALQQNGSS VLSEDKSKRL NTILNTMSTI YSTGKVCNPD NPQECLLLEP GLNEIMANSL DYNERLWAWE SWRSEVGKQL R PLYEEYVV LKNEMARANH YEDYGDYWRG DYEVNGVDGY DYSRGQLIED VEHTFEEIKP LYEHLHAYVR AKLMNAYPSY IS PIGCLPA HLLGDMWGRF WTNLYSLTVP FGQKPNIDVT DAMVDQAWDA QRIFKEAEKF FVSVGLPNMT QGFWENSMLT DPG NVQKAV CHPTAWDLGK GDFRILMCTK VTMDDFLTAH HEMGHIQYDM AYAAQPFLLR NGANEGFHEA VGEIMSLSAA TPKH LKSIG LLSPDFQEDN ETEINFLLKQ ALTIVGTLPF TYMLEKWRWM VFKGEIPKDQ WMKKWWEMKR EIVGVVEPVP HDETY CDPA SLFHVSNDYS FIRYYTRTLY QFQFQEALCQ AAKHEGPLHK CDISNSTEAG QKLFNMLRLG KSEPWTLALE NVVGAK NMN VRPLLNYFEP LFTWLKDQNK NSFVGWSTDW SPYADHHHHH HHH

UniProtKB: Angiotensin-converting enzyme 2

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Macromolecule #2: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 26.123621 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQPTESIVR FPNVTNLCPF HEVFNATRFA SVYAWNRTRI SNCVADYSVL YNFAPFFAFK CYGVSPTKLN DLCFTNVYAD SFVIKGNEV SQIAPGQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKHSG NYDYWYRLFR KSKLKPFERD ISTEIYQAGN K PCKGKGPN ...String:
RVQPTESIVR FPNVTNLCPF HEVFNATRFA SVYAWNRTRI SNCVADYSVL YNFAPFFAFK CYGVSPTKLN DLCFTNVYAD SFVIKGNEV SQIAPGQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKHSG NYDYWYRLFR KSKLKPFERD ISTEIYQAGN K PCKGKGPN CYFPLQSYGF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFHHHHHH

UniProtKB: Spike glycoprotein

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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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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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
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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 341631
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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