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- EMDB-56067: Polyclonal immune complex comprising SARS-CoV-2 spike (BA.2.87.1)... -

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Basic information

Entry
Database: EMDB / ID: EMD-56067
TitlePolyclonal immune complex comprising SARS-CoV-2 spike (BA.2.87.1) and a class 1 RBD-Down-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 (BA.2.87.1) spike
    • Protein or peptide: SARS-CoV-2 (BA.2.87.1)
KeywordsAntigen / antibody / complex / SARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus
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 12, 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_56067.png

Downloads & links

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Map

FileDownload / File: emd_56067.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-0.029233169 - 0.08675174
Average (Standard dev.)0.00060105696 (±0.006387949)
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 2 generated by 3D refinement of...

Fileemd_56067_half_map_1.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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Half map: Half map 1 generated by 3D refinement of...

Fileemd_56067_half_map_2.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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Sample components

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Entire : Polyclonal antibody complex with SARS-CoV-2 (BA.2.87.1) spike

EntireName: Polyclonal antibody complex with SARS-CoV-2 (BA.2.87.1) spike
Components
  • Complex: Polyclonal antibody complex with SARS-CoV-2 (BA.2.87.1) spike
    • Protein or peptide: SARS-CoV-2 (BA.2.87.1)

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Supramolecule #1: Polyclonal antibody complex with SARS-CoV-2 (BA.2.87.1) spike

SupramoleculeName: Polyclonal antibody complex with SARS-CoV-2 (BA.2.87.1) 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 (BA.2.87.1)

MacromoleculeName: SARS-CoV-2 (BA.2.87.1) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQSYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAISGTN DTKRFDNPVL PFNDGVYFAS TEKFNIIRGW IFGTTLDSKT QSLLIVNNAT NAVIKVCEFQ FKNNKSLMES EFRVYSSANN CTFEYVSQPF LMDLEGKQGN FKNLSEFVFK ...String:
MFVFLVLLPL VSSQSYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAISGTN DTKRFDNPVL PFNDGVYFAS TEKFNIIRGW IFGTTLDSKT QSLLIVNNAT NAVIKVCEFQ FKNNKSLMES EFRVYSSANN CTFEYVSQPF LMDLEGKQGN FKNLSEFVFK NIDGYFKIYS KHTPINLGRG LPQGFSALEP LVDLPIGINI TRFQTLLALH RSYLTPGDSS SGWTAGAAAY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKS FTVEKGIYQT SNFRVQPTES IVRFPNITNL CPFDEVFNAT RFASVYAWNR KRISNCVADY SVLYNFAPFF AFKCYGVSPT KLNDLCFTNV YADSFVIRGN EVSQIAPGQT GTIADYNYKL PDDFTGCVIA WNSNKLDSNG GGNYNYMYRL FRKSKLKPFE RDISTEIYQA GNTPCKGVAG FNCYFPLQSY GFRPTYGVGH QPYRVVVLSF ELLHAPATVC GPKKSTNLVK NKCVNFNFNG LTGTGVLTES NKKFLPFQQF GRDIADTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVSVAIH ADQLTPTWRV YSTGSNGFQT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTRSHGSAS SVASQPIIAY TMSLGAENSV AYSNNSIAIP TNFTISVTTE ILPVSMTKTS VDCTMYICGD STECSNLLLQ YGSFCTQLKR ALTGIAVEQD KNTQEVFAQV KQIYKIPPIK HFGGFNFSQI LPDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPALQ IPFPMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ GSLSSTPSAL GKLQDVVNHN AQALNTLVKQ LSSKFGAISS VLNDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDVVIGIVNN TVYDPLQPEL DSFKEELDKY FKNHTSPDVD LGDISGINAS VVNIQKEIDR LNEVAKNLNE SLIDLQELGK YEQGSGYIPE APRDGQAYVR KDGEWVLLST FLGRSLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSAWSHPQ FEK

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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: 1 / Number real images: 667 / 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: 404653
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: 565
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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