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- EMDB-45969: Local refinement of the SARS-CoV-2 BA.2.86 RBD in complex with TR... -

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Entry
Database: EMDB / ID: EMD-45969
TitleLocal refinement of the SARS-CoV-2 BA.2.86 RBD in complex with TRI2-2 minibinder
Map datasharpened map
Sample
  • Complex: SARS-CoV-2 BA.2.86 RBD in complex with TRI2-2 minibinder
    • Protein or peptide: BA.2.86 spike protein RBD
    • Protein or peptide: Pan-variant miniprotein TRI2-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSarbecoviruses / Spike glycoprotein / Structural Genomic / inhibitor / viral protein / minibinder / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Biological speciesSarbecovirus sp. / Severe acute respiratory syndrome coronavirus 2 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLee J / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158186 United States
CitationJournal: Commun Biol / Year: 2026
Title: The computationally designed TRI2-2 miniprotein inhibitor protects against multiple SARS-CoV-2 Omicron variants.
Authors: Jimin Lee / James Brett Case / Young-Jun Park / Rashmi Ravichandran / Daniel Asarnow / M Alejandra Tortorici / Jack T Brown / Shilpa Sanapala / Lauren Carter / David Baker / Michael S Diamond / David Veesler /
Abstract: The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has compromised neutralizing antibody responses elicited by prior infection or vaccination and abolished the ...The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has compromised neutralizing antibody responses elicited by prior infection or vaccination and abolished the utility of most monoclonal antibody therapeutics. We previously described a computationally-designed, homotrimeric miniprotein inhibitor, designated TRI2-2, that protects mice against pre-Omicron SARS-CoV-2 variants. Here, we show that TRI2-2 exhibits broadly neutralizing activity of SARS-CoV-2 variants and protects mice against BQ.1.1, XBB.1.5 and BA.2.86 challenge when administered intranasally post-exposure. The resistance of TRI2-2 to viral escape by most variants and the ability to deliver it directly to the upper airways highlight the potential of the multivalent miniprotein inhibitor as an alternative therapeutic modality.
History
DepositionJul 29, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45969.png

Downloads & links

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Map

FileDownload / File: emd_45969.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 512 pix.
= 512. Å		1 Å/pix.
x 512 pix.
= 512. Å		1 Å/pix.
x 512 pix.
= 512. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.18
Minimum - Maximum-4.1706095 - 6.8964477
Average (Standard dev.)-0.00018666222 (±0.04404094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 512.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_45969_additional_1.map
Annotationunsharpened map
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Half map: #2

Fileemd_45969_half_map_1.map
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Half map: #1

Fileemd_45969_half_map_2.map
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Sample components

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Entire : SARS-CoV-2 BA.2.86 RBD in complex with TRI2-2 minibinder

EntireName: SARS-CoV-2 BA.2.86 RBD in complex with TRI2-2 minibinder
Components
  • Complex: SARS-CoV-2 BA.2.86 RBD in complex with TRI2-2 minibinder
    • Protein or peptide: BA.2.86 spike protein RBD
    • Protein or peptide: Pan-variant miniprotein TRI2-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 BA.2.86 RBD in complex with TRI2-2 minibinder

SupramoleculeName: SARS-CoV-2 BA.2.86 RBD in complex with TRI2-2 minibinder
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Sarbecovirus sp.

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Macromolecule #1: BA.2.86 spike protein RBD

MacromoleculeName: BA.2.86 spike protein RBD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 21.95882 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLCPFHEVFN ATRFASVYAW NRTRISNCVA DYSVLYNFAP FFAFKCYGVS PTKLNDLCFT NVYADSFVIK GNEVSQIAPG QTGNIADYN YKLPDDFTGC VIAWNSNKLD SKHSGNYDYW YRLFRKSKLK PFERDISTEI YQAGNKPCKG KGPNCYFPLQ S YGFRPTYG ...String:
NLCPFHEVFN ATRFASVYAW NRTRISNCVA DYSVLYNFAP FFAFKCYGVS PTKLNDLCFT NVYADSFVIK GNEVSQIAPG QTGNIADYN YKLPDDFTGC VIAWNSNKLD SKHSGNYDYW YRLFRKSKLK PFERDISTEI YQAGNKPCKG KGPNCYFPLQ S YGFRPTYG VGHQPYRVVV LSFELLHAPA TVCGP

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Macromolecule #2: Pan-variant miniprotein TRI2-2

MacromoleculeName: Pan-variant miniprotein TRI2-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.565787 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ELEEQVMHVL DQVSELAHEL LHKLTGEELE RAAYFNWWAT EMMLELIKSD DEREIREIEE EARRILEHLE ELARKGGSEA LEELEKALR ELKKSTDELE RSTEELEKNP SEDALVENNR LIVENNKIIV EVLRIIAKVL KLEHHHHHH

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / 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: 53.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 299537
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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