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- EMDB-56058: Polyclonal immune complex comprising SARS-CoV-2 spike (Wuhan) and... -

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Basic information

Entry
Database: EMDB / ID: EMD-56058
TitlePolyclonal immune complex comprising SARS-CoV-2 spike (Wuhan) and a class 1 NTD-targeting antibody - Obtained by negative stain EM
Map dataMain map generated by 3D refinement of the particle subset corresponding to one polyclonal immune complex.
Sample
  • Complex: Polyclonal antibody complex with SARS-CoV-2 (Wuhan) spike
    • Protein or peptide: SARS-CoV-2 spike (Wuhan)
KeywordsAntigen / antibody / complex / SARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / negative staining / Resolution: 35.5 Å
AuthorsEray E / Antanasijevic A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Antigenic landscape of a highly mutated SARS-CoV-2 Spike in ongoing viral evolution
Authors: Turelli P / Eray E / Raclot C / Trono D / Antanasijevic A
History
DepositionDec 11, 2025-
Header (metadata) releaseOct 21, 2026-
Map releaseOct 21, 2026-
UpdateOct 21, 2026-
Current statusOct 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56058.png

Downloads & links

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Map

FileDownload / File: emd_56058.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map generated by 3D refinement of the particle subset corresponding to one polyclonal immune complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.44 Å/pix.
x 160 pix.
= 390.4 Å		2.44 Å/pix.
x 160 pix.
= 390.4 Å		2.44 Å/pix.
x 160 pix.
= 390.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.025629029 - 0.09015536
Average (Standard dev.)0.00015949877 (±0.006046154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 390.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 generated by 3D refinement of...

Fileemd_56058_half_map_1.map
AnnotationHalf map 1 generated by 3D refinement of the particle subset corresponding to one polyclonal immune complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 generated by 3D refinement of...

Fileemd_56058_half_map_2.map
AnnotationHalf map 2 generated by 3D refinement of the particle subset corresponding to one polyclonal immune complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Polyclonal antibody complex with SARS-CoV-2 (Wuhan) spike

EntireName: Polyclonal antibody complex with SARS-CoV-2 (Wuhan) spike
Components
  • Complex: Polyclonal antibody complex with SARS-CoV-2 (Wuhan) spike
    • Protein or peptide: SARS-CoV-2 spike (Wuhan)

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Supramolecule #1: Polyclonal antibody complex with SARS-CoV-2 (Wuhan) spike

SupramoleculeName: Polyclonal antibody complex with SARS-CoV-2 (Wuhan) spike
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus

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Macromolecule #1: SARS-CoV-2 spike (Wuhan)

MacromoleculeName: SARS-CoV-2 spike (Wuhan) / type: protein_or_peptide / ID: 1
Details: SARS-CoV-2 spike (Wuhan) ectodomain stabilized with Hexapro mutations
Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Wuhan
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQDVNCTEV PVAIHADQLT PTWRVYSTGS NVFQTRAGCL IGAEHVNNSY ECDIPIGAGI CASYQTQTNS PGSASSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLNRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKDFGGF NFSQILPDPS KPSKRSPIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GPALQIPFPM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLSS TPSALGKLQD VVNQNAQALN TLVKQLSSNF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVSGNCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELGKYEQ

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTrisTris
150.0 mMNaClSalt

Details: TBS
StainingType: NEGATIVE / Material: Uranyl formate / Details: 2% UF
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 0.5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR

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Electron microscopy

MicroscopeTFS TALOS L120C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Number grids imaged: 3 / Number real images: 1044 / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Talos L120C / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 396746
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: EM map generated by molmap command in chimera, low-pass filtered to 20 A
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 35.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 1456
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 8 / Software - Name: RELION

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