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- EMDB-50263: SARS-CoV-2 BA-2.87.1 Spike ectodomain -

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Basic information

Entry
Database: EMDB / ID: EMD-50263
TitleSARS-CoV-2 BA-2.87.1 Spike ectodomain
Map dataBA2-87.1 cryoEM map C3 symmetry
Sample
  • Complex: BA-2.87.1 variant SARS-CoV2 S protein
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsViral protein / immune system / SARS-CoV-2 / RBD / Spike / glycoprotein / BA.2.87.1 / receptor / coronavirus-2 / N-terminal domain / Supersite
Function / homology
Function and homology information


virion component / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion ...virion component / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Enterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRen J / Stuart DI / Duyvesteyn HME
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
Citation
Journal: Structure / Year: 2024
Title: Concerted deletions eliminate a neutralizing supersite in SARS-CoV-2 BA.2.87.1 spike.
Authors: Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / Chang Liu / Piyada Supasa / Barbara Kronsteiner / Katie Jeffery / Lizzie Stafford / Paul Klenerman / Susanna J Dunachie / / Juthathip ...Authors: Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / Chang Liu / Piyada Supasa / Barbara Kronsteiner / Katie Jeffery / Lizzie Stafford / Paul Klenerman / Susanna J Dunachie / / Juthathip Mongkolsapaya / Elizabeth E Fry / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: BA.2.87.1 represents a major shift in the BA.2 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is unusual in having two lengthy deletions of polypeptide in the spike (S) ...BA.2.87.1 represents a major shift in the BA.2 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is unusual in having two lengthy deletions of polypeptide in the spike (S) protein, one of which removes a beta-strand. Here we investigate its neutralization by a variety of sera from infected and vaccinated individuals and determine its spike (S) ectodomain structure. The BA.2.87.1 receptor binding domain (RBD) is structurally conserved and the RBDs are tightly packed in an "all-down" conformation with a small rotation relative to the trimer axis as compared to the closest previously observed conformation. The N-terminal domain (NTD) maintains a remarkably similar structure overall; however, the rearrangements resulting from the deletions essentially destroy the so-called supersite epitope and eliminate one glycan site, while a mutation creates an additional glycan site, effectively shielding another NTD epitope. BA.2.87.1 is relatively easily neutralized but acquisition of additional mutations in the RBD could increase antibody escape allowing it to become a dominant sub-lineage.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Authors: Liebschner D / Afonine PV
#2: Journal: Nature Methods / Year: 2017
Title: cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
Authors: Punjani A / Rubinstein JL
History
DepositionMay 9, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50263.png

Downloads & links

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Map

FileDownload / File: emd_50263.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBA2-87.1 cryoEM map C3 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 350 pix.
= 255.605 Å		0.73 Å/pix.
x 350 pix.
= 255.605 Å		0.73 Å/pix.
x 350 pix.
= 255.605 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: 0.0574
Minimum - Maximum-0.21243459 - 0.49160874
Average (Standard dev.)0.00041368767 (±0.019395774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 255.605 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: BA2-87.1 cryoEM half map C3 symmetry

Fileemd_50263_half_map_1.map
AnnotationBA2-87.1 cryoEM half map C3 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BA2-87.1 cryoEM half map C3 symmetry

Fileemd_50263_half_map_2.map
AnnotationBA2-87.1 cryoEM half map C3 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BA-2.87.1 variant SARS-CoV2 S protein

EntireName: BA-2.87.1 variant SARS-CoV2 S protein
Components
  • Complex: BA-2.87.1 variant SARS-CoV2 S protein
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BA-2.87.1 variant SARS-CoV2 S protein

SupramoleculeName: BA-2.87.1 variant SARS-CoV2 S protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Spike protein recombinantly expressed using sequence of human-derived BA-2.87.1 variant of SARS-CoV2.
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 139.502484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQSYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAISGTN DTKRFDNPVL PFNDGVYFAS TEKFNIIRG WIFGTTLDSK TQSLLIVNNA TNAVIKVCEF QFKNNKSLME SEFRVYSSAN NCTFEYVSQP FLMDLEGKQG N FKNLSEFV ...String:
MFVFLVLLPL VSSQSYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAISGTN DTKRFDNPVL PFNDGVYFAS TEKFNIIRG WIFGTTLDSK TQSLLIVNNA TNAVIKVCEF QFKNNKSLME SEFRVYSSAN NCTFEYVSQP FLMDLEGKQG N FKNLSEFV FKNIDGYFKI YSKHTPINLG RGLPQGFSAL EPLVDLPIGI NITRFQTLLA LHRSYLTPGD SSSGWTAGAA AY YVGYLQP RTFLLKYNEN GTITDAVDCA LDPLSETKCT LKSFTVEKGI YQTSNFRVQP TESIVRFPNI TNLCPFDEVF NAT RFASVY AWNRKRISNC VADYSVLYNF APFFAFKCYG VSPTKLNDLC FTNVYADSFV IRGNEVSQIA PGQTGTIADY NYKL PDDFT GCVIAWNSNK LDSNGGGNYN YMYRLFRKSK LKPFERDIST EIYQAGNTPC KGVAGFNCYF PLQSYGFRPT YGVGH QPYR VVVLSFELLH APATVCGPKK STNLVKNKCV NFNFNGLTGT GVLTESNKKF LPFQQFGRDI ADTTDAVRDP QTLEIL DIT PCSFGGVSVI TPGTNTSNQV AVLYQGVNCT EVSVAIHADQ LTPTWRVYST GSNGFQTRAG CLIGAEYVNN SYECDIP IG AGICASYQTQ TRSHGSASSV ASQPIIAYTM SLGAENSVAY SNNSIAIPTN FTISVTTEIL PVSMTKTSVD CTMYICGD S TECSNLLLQY GSFCTQLKRA LTGIAVEQDK NTQEVFAQVK QIYKIPPIKH FGGFNFSQIL PDPSKPSKRS FIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGAALQ IPFAMQMAYR FNGIGVTQN VLYENQKLIA NQFNSAIGKI QGSLSSTASA LGKLQDVVNH NAQALNTLVK QLSSKFGAIS SVLNDILSRL D PPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QSAPHGVVFL HV TYVPAQE KNFTTAPAIC HDGKAHFPRE GVFVSNGTHW FVTQRNFYEP QIITTDNTFV SGNCDVVIGI VNNTVYDPLQ PEL DSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDRLNEVAK NLNESLIDLQ ELGKYEQGSG YIPEAPRDGQ AYVR KDGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHGSA WSHPQFEKGG GSGGGSGGSA WSHPQFEK

UniProtKB: Spike glycoprotein, Fibritin

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 39 / 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

BufferpH: 7.4
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE
DetailsBA.2.87.1 Spike

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9818 / Average electron dose: 40.0 e/Å2 / Details: Images were collected in EER format.
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: 504319
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8r1c

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.4.3.1)
Details: Determined in cryosparc local resolution estimation module.
Number images used: 37441
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v.4.3.1)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. v.4.3.1) / Details: 3D classification without alignment in cryosparc.

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Atomic model buiding 1

Initial modelPDB ID:

8r1c


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsPhenix real space refinement with manual checks using coot.
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9f9y:
SARS-CoV-2 BA-2.87.1 Spike ectodomain

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