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- EMDB-14271: Structure of the SARS-CoV-2 spike glycoprotein in complex with th... -

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Entry
Database: EMDB / ID: EMD-14271
TitleStructure of the SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment (local refinement)
Map dataDeepEMhancer sharpened map
Sample
  • Complex: SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
    • Complex: SARS-CoV-2 spike proteinCoronavirus spike protein
      • Protein or peptide: SARS-CoV-2 spike proteinCoronavirus spike protein
    • Complex: FabFragment antigen-binding
      • Protein or peptide: 87G7 heavy chain variable domain
      • Protein or peptide: 87G7 light chain variable domain
KeywordsCoronavirus / Spike / Antibody / Complex / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsHurdiss DL / Drulyte I
Funding supportEuropean Union, Germany, 3 items
OrganizationGrant numberCountry
European Commission101003651European Union
German Research Foundation (DFG)398066876/GRK 2485/1 Germany
German Federal Ministry for Education and Research01KI1723G Germany
CitationJournal: Sci Immunol / Year: 2022
Title: An ACE2-blocking antibody confers broad neutralization and protection against Omicron and other SARS-CoV-2 variants of concern.
Authors: Wenjuan Du / Daniel L Hurdiss / Dubravka Drabek / Anna Z Mykytyn / Franziska K Kaiser / Mariana González-Hernández / Diego Muñoz-Santos / Mart M Lamers / Rien van Haperen / Wentao Li / ...Authors: Wenjuan Du / Daniel L Hurdiss / Dubravka Drabek / Anna Z Mykytyn / Franziska K Kaiser / Mariana González-Hernández / Diego Muñoz-Santos / Mart M Lamers / Rien van Haperen / Wentao Li / Ieva Drulyte / Chunyan Wang / Isabel Sola / Federico Armando / Georg Beythien / Malgorzata Ciurkiewicz / Wolfgang Baumgärtner / Kate Guilfoyle / Tony Smits / Joline van der Lee / Frank J M van Kuppeveld / Geert van Amerongen / Bart L Haagmans / Luis Enjuanes / Albert D M E Osterhaus / Frank Grosveld / Berend-Jan Bosch /
Abstract: The ongoing evolution of SARS-CoV-2 has resulted in the emergence of Omicron, which displays notable immune escape potential through mutations at key antigenic sites on the spike protein. Many of ...The ongoing evolution of SARS-CoV-2 has resulted in the emergence of Omicron, which displays notable immune escape potential through mutations at key antigenic sites on the spike protein. Many of these mutations localize to the spike protein ACE2 receptor binding domain, annulling the neutralizing activity of therapeutic antibodies that were effective against other variants of concern (VOCs) earlier in the pandemic. Here, we identified a receptor-blocking human monoclonal antibody, 87G7, that retained potent in vitro neutralizing activity against SARS-CoV-2 variants including the Alpha, Beta, Gamma, Delta, and Omicron (BA.1/BA.2) VOCs. Using cryo-electron microscopy and site-directed mutagenesis experiments, we showed that 87G7 targets a patch of hydrophobic residues in the ACE2-binding site that are highly conserved in SARS-CoV-2 variants, explaining its broad neutralization capacity. 87G7 protected mice and hamsters prophylactically against challenge with all current SARS-CoV-2 VOCs and showed therapeutic activity against SARS-CoV-2 challenge in both animal models. Our findings demonstrate that 87G7 holds promise as a prophylactic or therapeutic agent for COVID-19 that is more resilient to SARS-CoV-2 antigenic diversity.
History
DepositionFeb 8, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14271.png

Downloads & links

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Map

FileDownload / File: emd_14271.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 300 pix.
= 372. Å		1.24 Å/pix.
x 300 pix.
= 372. Å		1.24 Å/pix.
x 300 pix.
= 372. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.0018065077 - 3.370331
Average (Standard dev.)0.00022597187 (±0.011496915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14271_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Local resolution filtered map

Fileemd_14271_additional_1.map
AnnotationLocal resolution filtered map
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Additional map: Unsharpened map

Fileemd_14271_additional_2.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_14271_additional_3.map
AnnotationSharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_14271_half_map_1.map
AnnotationHalf map 1
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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_14271_half_map_2.map
AnnotationHalf map 2
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Sample components

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Entire : SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody F...

EntireName: SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
Components
  • Complex: SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
    • Complex: SARS-CoV-2 spike proteinCoronavirus spike protein
      • Protein or peptide: SARS-CoV-2 spike proteinCoronavirus spike protein
    • Complex: FabFragment antigen-binding
      • Protein or peptide: 87G7 heavy chain variable domain
      • Protein or peptide: 87G7 light chain variable domain

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Supramolecule #1: SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody F...

SupramoleculeName: SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 500 KDa

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Supramolecule #2: SARS-CoV-2 spike protein

SupramoleculeName: SARS-CoV-2 spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Fab

SupramoleculeName: Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SARS-CoV-2 spike protein

MacromoleculeName: SARS-CoV-2 spike protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
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 PAAARSVASQ 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 LEVLFQGPGH HHHHHHHSAW SHPQFEKGGG SGGGGSGGSA WSHPQFEK

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Macromolecule #2: 87G7 heavy chain variable domain

MacromoleculeName: 87G7 heavy chain variable domain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLLESGGG LVQPGGSLRL SCVASGFTFS SYVMSWVRQA PGKGLEWVAA ISGSGGNTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCAKEG TYYYGSGSFW GQGTLVTVSS

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Macromolecule #3: 87G7 light chain variable domain

MacromoleculeName: 87G7 light chain variable domain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPAT LSLSPGERAT LSCRASQSFH NYLAWYQQKP GRAPRLLIFD ASNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RFNWPLTFGG GTKVEIK

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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

Concentration4 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 3831 / Average electron dose: 51.5 e/Å2
Details: 1331 images collected from grid 1 (0.02% FOM) and 2500 images collected from grid 2 (0% FOM)
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 934811
Details: 313636 particles were picked from 1331 images from 0.02% FOM dataset and 621175 particles were picked from 2500 images without FOM.
Startup modelType of model: OTHER / Details: Generated ab initio using cryoSPARC
Initial angle assignmentType: RANDOM ASSIGNMENT
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.1)
Details: Particles were imported into Relion 3.1 and, using the relion particle symmetry expand tool, each particle from the C3 symmetry imposed reconstruction was assigned three orientations ...Details: Particles were imported into Relion 3.1 and, using the relion particle symmetry expand tool, each particle from the C3 symmetry imposed reconstruction was assigned three orientations corresponding to its symmetry related views. The soft mask was placed over a single RBD Fab region of the map, and the symmetry expanded particles were subjected to masked 3D classification without alignment using a regularization parameter (T number) of 20. Following a single round of focused classification, the best particle stack consisting of 72,118 particles was imported back to cryoSPARC for local refinement.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Software - details: Local refinement job
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 72118
FSC plot (resolution estimation)

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