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- EMDB-54814: KP.3 SARS-CoV2 with fab JN-1.6 local refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-54814
TitleKP.3 SARS-CoV2 with fab JN-1.6 local refinement
Map data
Sample
  • Complex: Trimeric complex of JN.1-9 fab with SARS-CoV2 KP.3 Spike glycoprotein subunit.
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: JN.1-6 antibody fragment heavy chain variable domain
    • Protein or peptide: JN.1-6 antibody fragment light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV2 / virus / complex / antibody / neutralising / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDuyvesteyn HME / Ren J / Stuart DI
Funding support China, United Kingdom, 2 items
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 HME / Stuart DI / Ren J
History
DepositionAug 19, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54814.png

Downloads & links

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Map

FileDownload / File: emd_54814.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 560 pix.
= 408.968 Å		0.73 Å/pix.
x 560 pix.
= 408.968 Å		0.73 Å/pix.
x 560 pix.
= 408.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7303 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.145
Minimum - Maximum-0.58515555 - 0.8491225
Average (Standard dev.)0.00003032159 (±0.009725131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 408.96802 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54814_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54814_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric complex of JN.1-9 fab with SARS-CoV2 KP.3 Spike glycopro...

EntireName: Trimeric complex of JN.1-9 fab with SARS-CoV2 KP.3 Spike glycoprotein subunit.
Components
  • Complex: Trimeric complex of JN.1-9 fab with SARS-CoV2 KP.3 Spike glycoprotein subunit.
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: JN.1-6 antibody fragment heavy chain variable domain
    • Protein or peptide: JN.1-6 antibody fragment light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Trimeric complex of JN.1-9 fab with SARS-CoV2 KP.3 Spike glycopro...

SupramoleculeName: Trimeric complex of JN.1-9 fab with SARS-CoV2 KP.3 Spike glycoprotein subunit.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Fab fragment from papain cleavage.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1
Details: BA.3.2.2 variant sequence, with classic modifications (2 prolines, removal of the furin site)
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 142.373812 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 CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNVTNLCPFH EVFNATRFAS VYAWNRTRIS NCVADYSVLY NFAPFFAFKC YGVSPTKLND LCFTNVYADS FVIK GNEVS QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKHSGN YDYWYRSLRK SKLKPFERDI STEIYQAGNK PCKGK GPNC YFPLESYGFR PTYGVGHQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNFNFNGLTG TGVLTKSNKK FLPFQQ FGR DIVDTTDAVR DPQTLEILDI TPCSFGGVSV ITPGTNTSNQ VAVLYQGVNC TEVSVAIHAD QLTPTWRVYS TGSNVFQ TR AGCLIGAEYV NNSYECDIPI GAGICASYQT QTKSRGSASS VASQSIIAYT MSLGAENSVA YSNNSIAIPT NFTISVTT E ILPVSMTKTS VDCTMYICGD STECSNLLLQ YGSFCTQLKR ALTGIAVEQD KNTQEVFAQV KQIYKTPPIK YFGGFNFSQ ILPDPSKPSK RSFIEDLLFN KVTLADAGFI KQYGDCLGDI AARDLICAQK FNGLTVLPPL LTDEMIAQYT SALLAGTITS GWTFGAGAA LQIPFAMQMA YRFNGIGVTQ NVLYENQKLI ANQFNSAIGK IQDSLFSTAS ALGKLQDVVN HNAQALNTLV K QLSSKFGA ISSVLNDILS RLDPPEAEVQ IDRLITGRLQ SLQTYVTQQL IRAAEIRASA NLAATKMSEC VLGQSKRVDF CG KGYHLMS FPQSAPHGVV FLHVTYVPAQ EKNFTTAPAI CHDGKAHFPR EGVFVSNGTH WFLTQRNFYE PQIITTDNTF VSG NCDVVI GIVNNTVYDP LQLELDSFKE ELDKYFKNHT SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELG KYEQG SGYIPEAPRD GQAYVRKDGE WVLLSTFLGR SLEVLFQGPG HHHHHHHHGS AWSHPQFEKG GGSGGGSGGS AWSHP QFEK

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Macromolecule #2: JN.1-6 antibody fragment heavy chain variable domain

MacromoleculeName: JN.1-6 antibody fragment heavy chain variable domain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.657276 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVQPGRSLRL SCTTSGFTFD DYAMSWVRQA PGKGLEWVGF IRSIPYGGTT EYAASVKGRF TISRDVSKSI AYLQMNSLK TEDTAVYYCT RYHYGPGRTD AFDIWGQGTM VTVSS

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Macromolecule #3: JN.1-6 antibody fragment light chain

MacromoleculeName: JN.1-6 antibody fragment light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.297387 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYELTQPPSV SVSPGQTASI TCSGVKLGDK YASWYQQKSG QSPVLVIYHD TKRPSGIPER FSGSNSGNTA TLTISGTQAM DEADYYCQA WDSNTAIFGT GTKVTVL

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / 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

Concentration1 mg/mL
BufferpH: 7.5 / Details: 1 x PBS at pH 7.5
GridModel: C-flat-2/1 / Material: COPPER / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 7574 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3729251 / Details: Template picking
CTF correctionSoftware - Name: cryoSPARC / Details: Cryosparc patch CTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Ab initio model from particle set, generated in cryosparc
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 130659
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC
Details: Ab initio instead of conventional classification, two rounds.

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Atomic model buiding 1

Initial model
PDB IDChain

8cim

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
DetailsInitial 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.
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 68
Output model

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

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