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- EMDB-18649: Local refinement of SARS-CoV-2 BA.2.86 Spike and XBB-7 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-18649
TitleLocal refinement of SARS-CoV-2 BA.2.86 Spike and XBB-7 Fab
Map dataSharpened map of BA.2.86 spike with XBB7 fab local refinement.
Sample
  • Complex: BA-2.86 variant SARS-CoV2 S protein complexed with XBB-7 fab.
    • Complex: XBB-7 fab
      • Protein or peptide: XBB-7 fab heavy chain
      • Protein or peptide: XBB-7 fab light chain
    • Complex: BA.2.86 variant SARS-CoV2 S protein
      • Protein or peptide: Spike glycoprotein,Fibritin
KeywordsViral protein/immune system / SARS-CoV-2 / XBB-7 / RBD / Spike / BA.2.86 / VIRAL PROTEIN
Function / homology
Function and homology information


virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, 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, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsRen J / Duyvesteyn HME / Stuart DI
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
CitationJournal: To Be Published
Title: The emerging BA.2.86 Omicron sub-lineage balances antibody escape and ACE2 affinity
Authors: Stuart DI / Liu C
History
DepositionOct 12, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18649.png

Downloads & links

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Map

FileDownload / File: emd_18649.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of BA.2.86 spike with XBB7 fab local refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 450 pix.
= 328.635 Å		0.73 Å/pix.
x 450 pix.
= 328.635 Å		0.73 Å/pix.
x 450 pix.
= 328.635 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: 0.0706
Minimum - Maximum-0.77619433 - 1.098626
Average (Standard dev.)-0.000015484584 (±0.016228793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 328.635 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of BA.2.86 spike with XBB7 fab local refinement.

Fileemd_18649_half_map_1.map
AnnotationHalf map of BA.2.86 spike with XBB7 fab local refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18649_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 : BA-2.86 variant SARS-CoV2 S protein complexed with XBB-7 fab.

EntireName: BA-2.86 variant SARS-CoV2 S protein complexed with XBB-7 fab.
Components
  • Complex: BA-2.86 variant SARS-CoV2 S protein complexed with XBB-7 fab.
    • Complex: XBB-7 fab
      • Protein or peptide: XBB-7 fab heavy chain
      • Protein or peptide: XBB-7 fab light chain
    • Complex: BA.2.86 variant SARS-CoV2 S protein
      • Protein or peptide: Spike glycoprotein,Fibritin

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Supramolecule #1: BA-2.86 variant SARS-CoV2 S protein complexed with XBB-7 fab.

SupramoleculeName: BA-2.86 variant SARS-CoV2 S protein complexed with XBB-7 fab.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Spike protein recombinantly expressed using sequence of human-derived BA-2.86 variant of SARS-CoV2. XBB7 fab recombinantely expressed from sequenced fab derived from convalescent sera.

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Supramolecule #2: XBB-7 fab

SupramoleculeName: XBB-7 fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Details: XBB-7 fab recombinantely expressed from sequenced fab derived from convalescent sera.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: BA.2.86 variant SARS-CoV2 S protein

SupramoleculeName: BA.2.86 variant SARS-CoV2 S protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Details: Spike protein recombinantly expressed using sequence of human-derived BA-2.86 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: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 142.385828 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 YDYWYRLFRK SKLKPFERDI STEIYQAGNK PCKGK GPNC YFPLQSYGFR PTYGVGHQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNFNFNGLTG TGVLTKSNKK FLPFQQ FGR DIVDTTDAVR DPQTLEILDI TPCSFGGVSV ITPGTNTSNQ VAVLYQGVNC TEVSVAIHAD QLTPTWRVYS TGSNVFQ TR AGCLIGAEYV NNSYECDIPI GAGVCASYQT QTKSHGSASS 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 WFVTQRNFYE PQIITTDNTF VSG NCDVVI GIVNNTVYDP LQLELDSFKE ELDKYFKNHT SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELG KYEQG SGYIPEAPRD GQAYVRKDGE WVLLSTFLGR SLEVLFQGPG HHHHHHHHGS AWSHPQFEKG GGSGGGSGGS AWSHP QFEK

UniProtKB: Spike glycoprotein, Fibritin

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Macromolecule #2: XBB-7 fab heavy chain

MacromoleculeName: XBB-7 fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.613259 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG LVQPGGSLRL SCAASGFIFR SFSMSWVRQA PGKGLEWVAN INEDGGEKYY VDSVKGRFTI SRDYAKDSVF LQMNSLRAE DTAVYYCARV GPYYYDSAGY YRRHYHFGMD VWGQGTTVTV SS

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Macromolecule #3: XBB-7 fab light chain

MacromoleculeName: XBB-7 fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.388351 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPASV SGSPGQSITI SCTGTSSDIG DYNYVSWYQQ HPGKAPKLMI LSNRFSGSKS GNTASLTISG LQAEDEADYY CSSYTGSVT VFGGGTKLTV L

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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.
VitrificationCryogen name: ETHANE
DetailsBA-2.86 Spike with XBB-7 fab in 6-fold excess of S protein.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9664 / Average electron dose: 50.0 e/Å2 / Details: Images were collected in EER format.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 524958
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8cim

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 8 / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: Determined by cryoSPARC. / Number images used: 75021

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Atomic model buiding 1

Initial modelPDB ID:

8cim


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-8qtd:
Local refinement of SARS-CoV-2 BA.2.86 Spike and XBB-7 Fab

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