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- PDB-9sf5: KP.3 SARS-CoV2 with fab JN-1.6 local refinement -

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Basic information

Entry
Database: PDB / ID: 9sf5
TitleKP.3 SARS-CoV2 with fab JN-1.6 local refinement
Components
  • JN.1-6 antibody fragment heavy chain variable domain
  • JN.1-6 antibody fragment light chain
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / SARS-CoV2 / virus / complex / antibody / neutralising
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDuyvesteyn, H.M.E. / Ren, J. / Stuart, D.I.
Funding support China, United Kingdom, 2items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Unusual broadly neutralising antibodies elicited by vaccine breakthrough infections by SARS-CoV-2 JN.1
Authors: Duyvesteyn, H.M.E. / Stuart, D.I. / Ren, J.
History
DepositionAug 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike glycoprotein
H: JN.1-6 antibody fragment heavy chain variable domain
L: JN.1-6 antibody fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,7715
Polymers167,3283
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Spike glycoprotein


Mass: 142373.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BA.3.2.2 variant sequence, with classic modifications (2 prolines, removal of the furin site)
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody JN.1-6 antibody fragment heavy chain variable domain


Mass: 13657.276 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody JN.1-6 antibody fragment light chain


Mass: 11297.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Trimeric complex of JN.1-9 fab with SARS-CoV2 KP.3 Spike glycoprotein subunit.
Type: COMPLEX / Details: Fab fragment from papain cleavage. / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5 / Details: 1 x PBS at pH 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7574

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
10PHENIX1.20.1_4487model refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
CTF correctionDetails: Cryosparc patch CTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3729251 / Details: Template picking
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130659 / Symmetry type: POINT
Atomic model buildingB value: 68 / Protocol: OTHER / Space: REAL
Details: Initial local fitting performed in ChimeraX then used two rounds of Phenix real space refinement (checking in coot in between), 3 iterations each with rigid body fitting and minimisation ...Details: Initial local fitting performed in ChimeraX then used two rounds of Phenix real space refinement (checking in coot in between), 3 iterations each with rigid body fitting and minimisation global, b-factor refinement during final round.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18CIM

8cim

18CIM1PDBexperimental model
21AlphaFoldin silico model
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023482
ELECTRON MICROSCOPYf_angle_d0.4024735
ELECTRON MICROSCOPYf_dihedral_angle_d8.5881237
ELECTRON MICROSCOPYf_chiral_restr0.04509
ELECTRON MICROSCOPYf_plane_restr0.004607

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