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- EMDB-73750: Structure of KP.3 spike in complex with Nanosota-9B (local refinement) -

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Basic information

Entry
Database: EMDB / ID: EMD-73750
TitleStructure of KP.3 spike in complex with Nanosota-9B (local refinement)
Map dataUnsharpened map of KP.3 spike in complex with Nb9B (local refinement)
Sample
  • Complex: KP.3 spike in complex with Nb9B
    • Protein or peptide: KP.3 spike
    • Protein or peptide: Nanosota-9B
KeywordsSARS-CoV-2 / entry / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsYe G / Bu F / Liu B / Li F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI171954 United States
CitationJournal: To Be Published
Title: Structure-Guided Nanobody Evolution Against SARS-CoV-2 Escape
Authors: Ye G / Bu F / Li F
History
DepositionNov 4, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73750.png

Downloads & links

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Map

FileDownload / File: emd_73750.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map of KP.3 spike in complex with Nb9B (local refinement)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 480 pix.
= 424.96 Å		0.89 Å/pix.
x 480 pix.
= 424.96 Å		0.89 Å/pix.
x 480 pix.
= 424.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88533 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.27832964 - 0.5413841
Average (Standard dev.)-0.00004107152 (±0.008607658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 424.95984 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map of KP.3 spike in complex with Nb9B (local refinement)

Fileemd_73750_additional_1.map
AnnotationSharpened map of KP.3 spike in complex with Nb9B (local refinement)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A map of KP.3 spike in complex with Nb9B (local refinement)

Fileemd_73750_half_map_1.map
AnnotationHalf_A map of KP.3 spike in complex with Nb9B (local refinement)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B map of KP.3 spike in complex with Nb9B (local refinement)

Fileemd_73750_half_map_2.map
AnnotationHalf_B map of KP.3 spike in complex with Nb9B (local refinement)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : KP.3 spike in complex with Nb9B

EntireName: KP.3 spike in complex with Nb9B
Components
  • Complex: KP.3 spike in complex with Nb9B
    • Protein or peptide: KP.3 spike
    • Protein or peptide: Nanosota-9B

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Supramolecule #1: KP.3 spike in complex with Nb9B

SupramoleculeName: KP.3 spike in complex with Nb9B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: KP.3 spike

MacromoleculeName: KP.3 spike / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 138.311781 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 QTKSRAGARS VASQSIIAYT MSLGAENSVA YSNNSIAIPT NFTISVTT E ILPVSMTKTS VDCTMYICGD STECSNLLLQ YGSFCTQLKR ALTGIAVEQD KNTQEVFAQV KQIYKTPPIK YFGGFNFSQ ILPDPSKPSK RSPIEDLLFN KVTLADAGFI KQYGDCLGDI AARDLICAQK FNGLTVLPPL LTDEMIAQYT SALLAGTITS GWTFGAGPA LQIPFPMQMA YRFNGIGVTQ NVLYENQKLI ANQFNSAIGK IQDSLFSTPS 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 KYEQY IKGSGYIPEA PRDGQAYVRK DGEWVLLSTF LGHHHHHH

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Macromolecule #2: Nanosota-9B

MacromoleculeName: Nanosota-9B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 16.304608 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQPGGSLRL SCTASGIALH SKATGWFRQA PGKEREGVSC ISSGDGTTYY EDSVEGRFTI SRDNAKNTVY LQMNSLKLE DTAVYYCAAD PSGVCHSGSY YYTDDDFYYR GQGTQVTVSS GGQHHHHHHG AYPYDVPDYA S

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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: GATAN K3 BIOQUANTUM (6k 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: 2.5 µm / Nominal defocus min: 0.75 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: PDB ENTRY
PDB model - PDB ID:

9co8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 95868
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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