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- EMDB-45971: Local refinement of the SARS-CoV-2 BA.2.86 NTD -

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Basic information

Entry
Database: EMDB / ID: EMD-45971
TitleLocal refinement of the SARS-CoV-2 BA.2.86 NTD
Map datasharpened map
Sample
  • Complex: SARS-CoV-2 BA.2.86 NTD
    • Protein or peptide: BA.2.86 Spike protein NTD
  • 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
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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 30, 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_45971.png

Downloads & links

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Map

FileDownload / File: emd_45971.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
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Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-5.78003 - 8.452277
Average (Standard dev.)-0.00018398346 (±0.051370163)
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_45971_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #1

Fileemd_45971_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45971_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : SARS-CoV-2 BA.2.86 NTD

EntireName: SARS-CoV-2 BA.2.86 NTD
Components
  • Complex: SARS-CoV-2 BA.2.86 NTD
    • Protein or peptide: BA.2.86 Spike protein NTD
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 BA.2.86 NTD

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

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Macromolecule #1: BA.2.86 Spike protein NTD

MacromoleculeName: BA.2.86 Spike protein NTD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 34.48702 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVMPLF NLITTTQSYT NSFTRGVYYP DKVFRSSVLH LTQDLFLPFF SNVTWFHAIS GTNGTKRFDN PVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVFIKV CEFQFCNDPF LDVYHKNNKS WMESESGVYS S ANNCTFEY ...String:
MFVFLVLLPL VSSQCVMPLF NLITTTQSYT NSFTRGVYYP DKVFRSSVLH LTQDLFLPFF SNVTWFHAIS GTNGTKRFDN PVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVFIKV CEFQFCNDPF LDVYHKNNKS WMESESGVYS S ANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI IGRDFPQGFS ALEPLVDLPI GINITRFQTL LA LNRSYLT PGDSSSGWTA GAADYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFT

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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: 3 / 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2330259
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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