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- EMDB-34120: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with ... -

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Entry
Database: EMDB / ID: EMD-34120
TitleCryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with golden hamster ACE2 (local refinement)
Map data
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with golden hamster ACE2 (local refinement)
    • Complex: Golden hamster angiotensin-converting enzyme 2
      • Protein or peptide: Angiotensin-converting enzyme
    • Complex: Omicron BA.2 RBD
      • Protein or peptide: Spike glycoprotein
  • 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


Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / angiotensin maturation / metallocarboxypeptidase activity / positive regulation of cardiac muscle contraction ...Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / angiotensin maturation / metallocarboxypeptidase activity / positive regulation of cardiac muscle contraction / brush border membrane / 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 / 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. / 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 ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesMesocricetus auratus (golden hamster) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 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
DepositionAug 18, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34120.png

Downloads & links

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Map

FileDownload / File: emd_34120.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 512 pix.
= 450.56 Å		0.88 Å/pix.
x 512 pix.
= 450.56 Å		0.88 Å/pix.
x 512 pix.
= 450.56 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017294677 - 2.0537128
Average (Standard dev.)0.00040122893 (±0.011895297)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_34120_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_34120_half_map_2.map
Projections & Slices
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Sample components

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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 golden hamster ACE2 (local refinement)
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with golden hamster ACE2 (local refinement)
    • Complex: Golden hamster angiotensin-converting enzyme 2
      • Protein or peptide: Angiotensin-converting enzyme
    • Complex: Omicron BA.2 RBD
      • Protein or peptide: Spike glycoprotein
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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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 golden hamster ACE2 (local refinement)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Golden hamster angiotensin-converting enzyme 2

SupramoleculeName: Golden hamster angiotensin-converting enzyme 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mesocricetus auratus (golden hamster)

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Supramolecule #3: Omicron BA.2 RBD

SupramoleculeName: Omicron BA.2 RBD / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Mesocricetus auratus (golden hamster)
Molecular weightTheoretical: 68.943328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SIIEEQAKTF LDKFNQEAED LSYQSALASW NYNTNITEEN AQKMNEAAAK WSAFYEEQSK LAKNYSLQEV QNLTIKRQLQ ALQQSGSSA LSADKNKQLN TILNTMSTIY STGKVCNPKN PQECLLLEPG LDDIMATSTD YNERLWAWEG WRAEVGKQLR P LYEEYVVL ...String:
SIIEEQAKTF LDKFNQEAED LSYQSALASW NYNTNITEEN AQKMNEAAAK WSAFYEEQSK LAKNYSLQEV QNLTIKRQLQ ALQQSGSSA LSADKNKQLN TILNTMSTIY STGKVCNPKN PQECLLLEPG LDDIMATSTD YNERLWAWEG WRAEVGKQLR P LYEEYVVL KNEMARANNY EDYGDYWRGD YEAEGADGYN YNGNQLIEDV ERTFKEIKPL YEQLHAYVRT KLMNTYPSYI SP TGCLPAH LLGDMWGRFW TNLYPLTVPF GQKPNIDVTD AMVNQGWNAE RIFKEAEKFF VSVGLPYMTQ GFWENSMLTD PGD DRKVVC HPTAWDLGKG DFRIKMCTKV TMDNFLTAHH EMGHIQYDMA YATQPFLLRN GANEGFHEAV GEIMSLSAAT PEHL KSIGL LPSDFQEDNE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGDIPKEQW MEKWWEMKRE IVGVVEPLPH DETYC DPAA LFHVSNDYSF IRYYTRTIYQ FQFQEALCQA AKHDGPLHKC DISNSTEAGQ KLLNMLRLGK SEPWTLALEN VVGARN MDV RPLLNYFEPL SVWLKEQNKN SFVGWNTDWS PYA

UniProtKB: Angiotensin-converting enzyme

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Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / 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: 22.282211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ITNLCPFDEV FNATRFASVY AWNRKRISNC VADYSVLYNF APFFAFKCYG VSPTKLNDLC FTNVYADSFV IRGNEVSQIA PGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGNKPC NGVAGFNCYF P LRSYGFRP ...String:
ITNLCPFDEV FNATRFASVY AWNRKRISNC VADYSVLYNF APFFAFKCYG VSPTKLNDLC FTNVYADSFV IRGNEVSQIA PGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGNKPC NGVAGFNCYF P LRSYGFRP TYGVGHQPYR VVVLSFELLH APATVCGPK

UniProtKB: Spike glycoprotein

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Macromolecule #3: ZINC ION

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

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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: 6 / 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 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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

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

7knb

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 224458
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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