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- EMDB-49907: JN.1.11+S31deletion spike with 1 missing RBD -

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Basic information

Entry
Database: EMDB / ID: EMD-49907
TitleJN.1.11+S31deletion spike with 1 missing RBD
Map data
Sample
  • Complex: JN.1.11+S31deletion spike with 1 missing RBD
KeywordsSARS-CoV-2 / COVID-19 / SPIKE / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsFeng Z / Huang J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Cell Rep / Year: 2025
Title: Structural and functional insights into the evolution of SARS-CoV-2 KP.3.1.1 spike protein.
Authors: Ziqi Feng / Jiachen Huang / Sabyasachi Baboo / Jolene K Diedrich / Sandhya Bangaru / James C Paulson / John R Yates / Meng Yuan / Ian A Wilson / Andrew B Ward /
Abstract: The JN.1-sublineage KP.3.1.1 recently emerged as the globally prevalent SARS-CoV-2 variant, demonstrating increased infectivity and antibody escape. We investigate how mutations and a deletion in the ...The JN.1-sublineage KP.3.1.1 recently emerged as the globally prevalent SARS-CoV-2 variant, demonstrating increased infectivity and antibody escape. We investigate how mutations and a deletion in the KP.3.1.1 spike protein (S) affect hACE2 binding and antibody escape. Mass spectrometry confirms a new glycan site at residue N30 that alters the glycoforms at neighboring N61. Cryoelectron microscopy (cryo-EM) structures show that the N30 glycan and rearrangement of adjacent residues do not significantly change the overall spike structure, up-down ratio of receptor-binding domains (RBDs), or hACE2 binding. Furthermore, a KP.3.1.1 S with hACE2 structure further confirms an epistatic effect between F456L and Q493E on hACE2 binding. Our analysis shows that SARS-CoV-2 variants that emerged after late 2023 are now incorporating reversions to residues found in other sarbecoviruses, including the N30 glycan, Q493E, and others. Overall, these results inform on the structural and functional consequences of the KP.3.1.1 mutations, the current SARS-CoV-2 evolutionary trajectory, and immune evasion.
History
DepositionMar 25, 2025-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49907.png

Downloads & links

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Map

FileDownload / File: emd_49907.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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AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.49273813 - 0.8047386
Average (Standard dev.)-0.00025491684 (±0.020227535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 367.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49907_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_49907_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49907_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : JN.1.11+S31deletion spike with 1 missing RBD

EntireName: JN.1.11+S31deletion spike with 1 missing RBD
Components
  • Complex: JN.1.11+S31deletion spike with 1 missing RBD

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Supramolecule #1: JN.1.11+S31deletion spike with 1 missing RBD

SupramoleculeName: JN.1.11+S31deletion spike with 1 missing RBD / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: JN.1.11

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 44.84 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8y18

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40728
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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