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- EMDB-54176: CryoEM structure of the spike S protein trimer of the omicron BA.... -

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Basic information

Entry
Database: EMDB / ID: EMD-54176
TitleCryoEM structure of the spike S protein trimer of the omicron BA.1 variant prepared in the presence of compound II-Na salt
Map data
Sample
  • Complex: Spike from OMICRON_GSAS_2P BA.1 variant
    • Protein or peptide: Spike from OMICRON_GSAS_2P BA.1 variant
KeywordsSpike / Omicron / SARS-CoV-2 / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSARS-CoV-2 (virus) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 6.25 Å
AuthorsLlacer JL / Lopez ML
Funding support Spain, 2 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-120322RB-C21 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-116880GB-I00 Spain
CitationJournal: ACS Omega / Year: 2025
Title: A Tetrapodal Tryptophan Derivative with Multiple Exposed Free Carboxylic Acids Blocks Host Cell Entry of Omicron SARS-Cov-2 and Respiratory Syncytial Virus.
Authors: Olaia Martí-Marí / Marta Moreno-Simoni / Ana Isabel Avilés-Alía / Luciana Rusu / Alicia Forcada-Nadal / Anmol Adhav / Maria Luisa López-Redondo / Ana-Belén Blázquez / Ana Esteban / ...Authors: Olaia Martí-Marí / Marta Moreno-Simoni / Ana Isabel Avilés-Alía / Luciana Rusu / Alicia Forcada-Nadal / Anmol Adhav / Maria Luisa López-Redondo / Ana-Belén Blázquez / Ana Esteban / Nereida Jiménez de Oya / Alberto Marina / Vicente Rubio / José Luis Llácer / Federico Gago / Miguel A Martín-Acebes / María-Jesús Pérez-Pérez / Ron Geller / Ana San-Félix /
Abstract: Omicron sublineages of SARS-CoV-2 have accelerated the spread of the virus and facilitated immune escape. In this work, we demonstrate that compound , a potent HIV and enterovirus A71 (EV-A71) entry ...Omicron sublineages of SARS-CoV-2 have accelerated the spread of the virus and facilitated immune escape. In this work, we demonstrate that compound , a potent HIV and enterovirus A71 (EV-A71) entry inhibitor previously discovered in our research group, also displays potent activity against different SARS-CoV-2 Omicron variants while showing no activity against the ancestral SARS-CoV-2 Wuhan strain. Moreover, its sodium salt () exhibited antiviral activity in a murine model of Omicron BA.1. infection. Indeed, biophysical and cryo-EM studies revealed binding of to the Omicron BA.1 spike (S) protein stabilizing a "closed" form in which ∼75% of the S particles have all RBDs down, unlike the usual "open" form with one RBD up. Such "closed" form decreases S avidity for the cellular receptor ACE2, thus inhibiting viral entry. Computer-assisted modeling studies strongly suggest that can interact with the intersubunit cavity of the S trimer of the Omicron BA.1 subvariant, making use of the multivalency principle. In this context, compound can be considered a pharmacological tool for studying and validating new antiviral strategies against Omicron variants. We also identified as a potent inhibitor of RSV and the Ebola virus. The effectiveness of against a diverse set of viruses of different families supports its use as a promising lead for the development of entry inhibitors against current and future viral infections, representing a meaningful advance in the field.
History
DepositionJun 25, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54176.png

Downloads & links

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Map

FileDownload / File: emd_54176.map.gz / Format: CCP4 / Size: 454.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 492 pix.
= 457.56 Å		0.93 Å/pix.
x 492 pix.
= 457.56 Å		0.93 Å/pix.
x 492 pix.
= 457.56 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.062271476 - 0.8515294
Average (Standard dev.)0.002518996 (±0.031966142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions492492492
Spacing492492492
CellA=B=C: 457.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map using DeepEMhancer

Fileemd_54176_additional_1.map
AnnotationSharpened map using DeepEMhancer
Projections & Slices
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Half map: #2

Fileemd_54176_half_map_1.map
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Half map: #1

Fileemd_54176_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Spike from OMICRON_GSAS_2P BA.1 variant

EntireName: Spike from OMICRON_GSAS_2P BA.1 variant
Components
  • Complex: Spike from OMICRON_GSAS_2P BA.1 variant
    • Protein or peptide: Spike from OMICRON_GSAS_2P BA.1 variant

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Supramolecule #1: Spike from OMICRON_GSAS_2P BA.1 variant

SupramoleculeName: Spike from OMICRON_GSAS_2P BA.1 variant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: SARS-CoV-2 Spike protein variant OMICRON with furin side replaced by GSAS and with 2 Proline substitution at 986 and 987
Source (natural)Organism: SARS-CoV-2 (virus)

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Macromolecule #1: Spike from OMICRON_GSAS_2P BA.1 variant

MacromoleculeName: Spike from OMICRON_GSAS_2P BA.1 variant / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: M F V F L V L L P L V S S Q C V N L T T R T Q L P P A Y T N S F T R G V Y Y P D K V F R S S V L H S T Q D L F L P F F S N V T W F H V I S G T N G T K R F D N P V L P F N D G ...String:
M F V F L V L L P L V S S Q C V N L T T R T Q L P P A Y T N S F T R G V Y Y P D K V F R S S V L H S T Q D L F L P F F S N V T W F H V I S G T N G T K R F D N P V L P F N D G V Y F A S I E K S N I I R G W I F G T T L D S K T Q S L L I V N N A T N V V I K V C E F Q F C N D P F L D H K N N K S W M E S E F R V Y S S A N N C T F E Y V S Q P F L M D L E G K Q G N F K N L R E F V F K N I D G Y F K I Y S K H T P I I V R E P E D L P Q G F S A L E P L V D L P I G I N I T R F Q T L L A L H R S Y L T P G D S S S G W T A G A A A Y Y V G Y L Q P R T F L L K Y N E N G T I T D A V D C A L D P L S E T K C T L K S F T V E K G I Y Q T S N F R V Q P T E S I V R F P N I T N L C P F D E V F N A T R F A S V Y A W N R K R I S N C V A D Y S V L Y N L A P F F T F K C Y G V S P T K L N D L C F T N V Y A D S F V I R G D E V R Q I A P G Q T G N I A D Y N Y K L P D D F T G C V I A W N S N K L D S K V S G N Y N Y L Y R L F R K S N L K P F E R D I S T E I Y Q A G N K P C N G V A G F N C Y F P L R S Y S F R P T Y G V G H Q P Y R V V V L S F E L L H A P A T V C G P K K S T N L V K N K C V N F N F N G L K G T G V L T E S N K K F L P F Q Q F G R D I A D T T D A V R D P Q T L E I L D I T P C S F G G V S V I T P G T N T S N Q V A V L Y Q G V N C T E V P V A I H A D Q L T P T W R V Y S T G S N V F Q T R A G C L I G A E Y V N N S Y E C D I P I G A G I C A S Y Q T Q T K S H G S A S S V A S Q S I I A Y T M S L G A E N S V A Y S N N S I A I P T N F T I S V T T E I L P V S M T K T S V D C T M Y I C G D S T E C S N L L L Q Y G S F C T Q L K R A L T G I A V E Q D K N T Q E V F A Q V K Q I Y K T P P I K Y F G G F N F S Q I L P D P S K P S K R S F I E D L L F N K V T L A D A G F I K Q Y G D C L G D I A A R D L I C A Q K F K G L T V L P P L L T D E M I A Q Y T S A L L A G T I T S G W T F G A G A A L Q I P F A M Q M A Y R F N G I G V T Q N V L Y E N Q K L I A N Q F N S A I G K I Q D S L S S T A S A L G K L Q D V V N H N A Q A L N T L V K Q L S S K F G A I S S V L N D I F S R L D P P E A E V Q I D R L I T G R L Q S L Q T Y V T Q Q L I R A A E I R A S A N L A A T K M S E C V L G Q S K R V D F C G K G Y H L M S F P Q S A P H G V V F L H V T Y V P A Q E K N F T T A P A I C H D G K A H F P R E G V F V S N G T H W F V T Q R N F Y E P Q I I T T D N T F V S G N C D V V I G I V N N T V Y D P L Q P E L D S F K E E L D K Y F K N H T S P D V D L G D I S G I N A S V V N I Q K E I D R L N E V A K N L N E S L I D L Q E L G K Y E Q

UniProtKB: Spike glycoprotein

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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

Concentration0.5 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 291.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5972 / Average exposure time: 5.01 sec. / Average electron dose: 36.55 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 451475
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Scipion / Number images used: 97694
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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