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- EMDB-64085: Local refinement of NTD and RBD domains of SARS-CoV2 KP.3.1.1 spi... -

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Entry
Database: EMDB / ID: EMD-64085
TitleLocal refinement of NTD and RBD domains of SARS-CoV2 KP.3.1.1 spike protein
Map dataLocal refinement of NTD and RBD domains of SARS-CoV2 KP.3.1.1 spike protein
SampleCryo-EM structure of SARS-CoV2 KP.3.1.1 spike protein != Severe acute respiratory syndrome coronavirus 2

Cryo-EM structure of SARS-CoV2 KP.3.1.1 spike protein

  • Virus: Severe acute respiratory syndrome coronavirus 2
    • Protein or peptide: SARS-CoV2 KP.3.1.1 spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSpike glycoprotein / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsHe MZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32401012 China
CitationJournal: Nat Commun / Year: 2025
Title: Pathogenicity, virological features, and immune evasion of SARS-CoV-2 JN.1-derived variants including JN.1.7, KP.2, KP.3, and KP.3.1.1.
Authors: Jialu Shi / Xiaoyu Zhao / Xiaohui Jin / Jiayan Li / Yuanchen Liu / Huan Liu / Ye-Fan Hu / Zhe Chen / Yuxin Xiao / Lei Wang / Yajie Wang / Yixin He / Yue Chai / Bingjie Hu / Huiping Shuai / ...Authors: Jialu Shi / Xiaoyu Zhao / Xiaohui Jin / Jiayan Li / Yuanchen Liu / Huan Liu / Ye-Fan Hu / Zhe Chen / Yuxin Xiao / Lei Wang / Yajie Wang / Yixin He / Yue Chai / Bingjie Hu / Huiping Shuai / Yang Wang / Xiangnan Li / Shujun Jiang / Yanliang Zhang / Xiaojuan Zhang / Wan-Mui Chan / Lin-Lei Chen / Jian-Piao Cai / Baokun Sui / Honglei Zhang / Dong Yang / Longchao Zhu / Shuofeng Yuan / Jie Zhou / Jian-Dong Huang / Kwok-Yung Yuen / Kelvin Kai-Wang To / Jasper Fuk-Woo Chan / Bao-Zhong Zhang / Qiao Wang / Maozhou He / Lei Sun / Pengfei Wang / Hin Chu /
Abstract: KP.3.1.1 became a dominant successor to JN.1 by the second half of 2024 but the intrinsic pathogenicity and virological feature of KP.3.1.1 remain incompletely understood. Here, we comprehensively ...KP.3.1.1 became a dominant successor to JN.1 by the second half of 2024 but the intrinsic pathogenicity and virological feature of KP.3.1.1 remain incompletely understood. Here, we comprehensively evaluated the pathogenesis and characteristics of KP.3.1.1 in comparison to JN.1 and other JN.1-derived variants including JN.1.7, KP.2, and KP.3. The unique S31del mutation on KP.3.1.1 spike confers further evasion to the clinically authorized mAb Pemivibart and reduces convalescent serum neutralization efficiency. Structural analysis indicates that S31del induces novel glycosylation sites that facilitates evasion of neutralizing antibodies. We further reveal that S31del significantly enhances pseudovirus entry efficiency in all evaluated cell types including the human primary nasal epithelial cells. Nevertheless, the intrinsic pathogenicity of KP.3.1.1 is similar to JN.1 and KP.3, and higher than that of JN.1.7 and KP.2 in a male hamster model. Interestingly, the increased virus infectivity conferred by S31del in KP.3.1.1 spike is counterbalanced by the NSP10 S33C mutation. Overall, our study indicates that a single spike mutation can confer both enhanced immune escape and increased viral infectivity. The opposing effects of spike and non-spike mutations highlight the complex interplay of viral genomic elements in shaping their overall fitness, and reveal the high plasticity of coronavirus evolution.
History
DepositionApr 8, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64085.png

Downloads & links

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Map

FileDownload / File: emd_64085.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement of NTD and RBD domains of SARS-CoV2 KP.3.1.1 spike protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 400 pix.
= 304. Å		0.76 Å/pix.
x 400 pix.
= 304. Å		0.76 Å/pix.
x 400 pix.
= 304. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.347
Minimum - Maximum-0.00085048494 - 2.546789
Average (Standard dev.)0.001932533 (±0.033216294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 304.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64085_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_64085_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64085_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 : Cryo-EM structure of SARS-CoV2 KP.3.1.1 spike protein

EntireName: Cryo-EM structure of SARS-CoV2 KP.3.1.1 spike protein
Components
  • Virus: Severe acute respiratory syndrome coronavirus 2
    • Protein or peptide: SARS-CoV2 KP.3.1.1 spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Severe acute respiratory syndrome coronavirus 2

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2697049
Sci species name: Severe acute respiratory syndrome coronavirus 2
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: SARS-CoV2 KP.3.1.1 spike glycoprotein

MacromoleculeName: SARS-CoV2 KP.3.1.1 spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 144.601125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAQCVNLI TTTQSYTNFT RGVYYPDKVF RSSVLHLTQD LFLPFFSNVT WFHAISGTNG TKRFDNPVL PFNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NFVIKVCEFQ FCNDPFLDVY HKNNKSWMES E SGVYSSAN ...String:
MPMGSLQPLA TLYLLGMLVA SVLAQCVNLI TTTQSYTNFT RGVYYPDKVF RSSVLHLTQD LFLPFFSNVT WFHAISGTNG TKRFDNPVL PFNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NFVIKVCEFQ FCNDPFLDVY HKNNKSWMES E SGVYSSAN NCTFEYVSQP FLMDLEGKQG NFKNLREFVF KNIDGYFKIY SKHTPIIQRD FPQGFSALEP LVDLPIGINI TR FQTLLAL NRSYLTPGDS SSGWTAGAAD YYVGYLQPRT FLLKYNENGT ITDAVDCALD PLSETKCTLK SFTVEKGIYQ TSN FRVQPT ESIVRFPNVT NLCPFHEVFN ATRFASVYAW NRTRISNCVA DYSVLYNFAS FSTFKCYGVS PTKLNDLCFT NVYA DSFVI KGNEVSQIAP GQTGNIADYN YKLPDDFTGC VIAWNSNKLD SKHSGNYDYW YRSLRKSKLK PFERDISTEI YQAGN KPCK GKGPNCYFPL ESYGFRPTYG VGHQPYRVVV LSFELLHAPA TVCGPKKSTN LVKNKCVNFN FNGLTGTGVL TKSNKK FLP FQQFGRDIVD TTDAVRDPQT LEILDITPCS FGGVSVITPG TNTSNQVAVL YQGVNCTEVS VAIHADQLTP TWRVYST GS NVFQTRAGCL IGAEYVNNSY ECDIPIGAGV CASYQTQTKS RGSASSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNF T ISVTTEILPV SMTKTSVDCT MYICGDSTEC SNLLLQYGSF CTQLKRALTG IAVEQDKNTQ EVFAQVKQIY KTPPIKYFG GFNFSQILPD PSKPSKRSPI EDLLFNKVTL ADAGFIKQYG DCLGDIAARD LICAQKFNGL TVLPPLLTDE MIAQYTSALL AGTITSGWT FGAGPALQIP FPMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LFSTPSALGK LQDVVNHNAQ A LNTLVKQL SSKFGAISSV LNDILSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SK RVDFCGK GYHLMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFLT QRNFYEPQII TTD NTFVSG NCDVVIGIVN NTVYDPLQLE LDSFKEELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLI DLQEL GKYEQGSGYI PEAPRDGQAY VRKDGEWVFL STFLSGLEVL FQGPGGWSHP QFEKGGGSGG GSGGSAWSHP QFEKG GSGL NDIFEAQKIE WHEHHHHHHH H

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 7 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36563
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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