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- EMDB-29054: SARS-CoV-2 Spike Hexapro - C68.59 Fab (Class 2 - Fab bound) -

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Basic information

Entry
Database: EMDB / ID: EMD-29054
TitleSARS-CoV-2 Spike Hexapro - C68.59 Fab (Class 2 - Fab bound)
Map dataSars-CoV-2 Spike Hexapro C59.68 Fab (Class 2 - Fab bound)
Sample
  • Organelle or cellular component: Sars-CoV-2 Hexapro
    • Protein or peptide: SARS-CoV-2 Spike Hexapro
    • Protein or peptide: C68.59 Fab Heavy Chain
    • Protein or peptide: C68.59 Fab Light Chain
Keywordsspike / fusion / membrane / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.72 Å
AuthorsCroft JT / Lee KK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01AI165808 United States
CitationJournal: bioRxiv / Year: 2023
Title: Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection.
Authors: Jamie Guenthoer / Michelle Lilly / Tyler N Starr / Bernadeta Dadonaite / Klaus N Lovendahl / Jacob T Croft / Caitlin I Stoddard / Vrasha Chohan / Shilei Ding / Felicitas Ruiz / Mackenzie S ...Authors: Jamie Guenthoer / Michelle Lilly / Tyler N Starr / Bernadeta Dadonaite / Klaus N Lovendahl / Jacob T Croft / Caitlin I Stoddard / Vrasha Chohan / Shilei Ding / Felicitas Ruiz / Mackenzie S Kopp / Andr S Finzi / Jesse D Bloom / Helen Y Chu / Kelly K Lee / Julie Overbaugh
Abstract: The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly ...The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs through BA.4/BA.5 in both pseudovirus-based and authentic virus assays. Three mAbs also retain potency to recently circulating VOCs XBB.1.5 and BQ.1.1 and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are novel in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.
History
DepositionDec 9, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29054.png

Downloads & links

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Map

FileDownload / File: emd_29054.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSars-CoV-2 Spike Hexapro C59.68 Fab (Class 2 - Fab bound)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.37 Å/pix.
x 120 pix.
= 404.64 Å		3.37 Å/pix.
x 120 pix.
= 404.64 Å		3.37 Å/pix.
x 120 pix.
= 404.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.372 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0332
Minimum - Maximum-0.06285492 - 0.21347202
Average (Standard dev.)-0.00016284871 (±0.008120654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 404.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Sars-CoV-2 Spike Hexapro C59.68 Fab (Class 2 - Fab bound) half map 1

Fileemd_29054_half_map_1.map
AnnotationSars-CoV-2 Spike Hexapro C59.68 Fab (Class 2 - Fab bound) half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Sars-CoV-2 Spike Hexapro C59.68 Fab (Class 2 - Fab bound) half map 1

Fileemd_29054_half_map_2.map
AnnotationSars-CoV-2 Spike Hexapro C59.68 Fab (Class 2 - Fab bound) half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Sars-CoV-2 Hexapro

EntireName: Sars-CoV-2 Hexapro
Components
  • Organelle or cellular component: Sars-CoV-2 Hexapro
    • Protein or peptide: SARS-CoV-2 Spike Hexapro
    • Protein or peptide: C68.59 Fab Heavy Chain
    • Protein or peptide: C68.59 Fab Light Chain

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Supramolecule #1: Sars-CoV-2 Hexapro

SupramoleculeName: Sars-CoV-2 Hexapro / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Sars-CoV-2 Hexapro, recombinantly expressed and purified.
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Location in cell: Virus surface protein

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Macromolecule #1: SARS-CoV-2 Spike Hexapro

MacromoleculeName: SARS-CoV-2 Spike Hexapro / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
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 QELGKYEQGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGRS LEVLFQGPGS GGGRGVPHIV MVDAYKRYKG GGSAWSHPQF EKGGGSGGGS GGSAWSHPQF EK

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Macromolecule #2: C68.59 Fab Heavy Chain

MacromoleculeName: C68.59 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LIQPGGSLRL SCAASGLTFT NYWMLWVRQA PGKGLVWVSH INSDGSSTNN ADSVKGRFT ISRDNAKNTL YLQMNSLRDE DTAVYYCGGT YCTGGSCGIV YWGQGTLVTV S S

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Macromolecule #3: C68.59 Fab Light Chain

MacromoleculeName: C68.59 Fab Light Chain / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
YELTQPPSVS VSPGQTASIT CSGDKLGDKY VFWYQQKSGQ SPALVIYQDS LRPSGIPDRF SGSNAGNTA TLTISGTPAV DEADYYCQAW DSSTLVFGGG TKLTVL

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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

Concentration2.25 mg/mL
BufferpH: 7.5 / Details: HEPES Buffered Saline: 50 mM HEPES, 280 mM NaCl
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.0 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 0, blot time 4s.
DetailsCombined with 17 uM C68.59 FAb (this class of particles did not display FAb density

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 3043 / Average exposure time: 2.397 sec. / Average electron dose: 50.0 e/Å2
Details: Images collected in movie mode at 0.03 second frames in super-resolution mode
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
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: 604558 / Details: CNN-particle picking with Cryolo
Startup modelType of model: OTHER
Details: Initial model determined ab-initio via initial model generation in Relion-4.0.
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 6.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 89935
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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