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- EMDB-22739: CryoEM reconstruction of SARS-CoV-2 Spike in complex with the Fab... -

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Basic information

Entry
Database: EMDB / ID: EMD-22739
TitleCryoEM reconstruction of SARS-CoV-2 Spike in complex with the Fab fragment of neutralizing antibody 80.
Map dataCryoEM reconstruction of SARS-CoV-2 Spike in complex with the Fab fragment of neutralizing antibody 80
Sample
  • Complex: SARS-CoV-2 Spike in complex with the Fab fragment of neutralizing antibody 80
    • Complex: Fab fragment of neutralizing antibody 80
      • Protein or peptide: Fab 80 heavy chain
      • Protein or peptide: Fab 80 light chain
    • Complex: SARS-CoV-2 Spike
      • Protein or peptide: SARS-CoV-2 Spike
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsKucharska I / Tan YZ / Benlekbir S / Rubinstein JL / Julien JP
Funding support Canada, 5 items
OrganizationGrant numberCountry
Ontario Ministry of Colleges and UniversitiesCOVID-19 Research Fund C-094-2424972-JULIEN Canada
Canada Foundation for Innovation Canada
Ontario Research Fund Canada
The Hospital For Sick Children Foundation Canada
Canada Research Chairs program Canada
Citation
Journal: Nat Commun / Year: 2021
Title: Multivalency transforms SARS-CoV-2 antibodies into ultrapotent neutralizers.
Authors: Edurne Rujas / Iga Kucharska / Yong Zi Tan / Samir Benlekbir / Hong Cui / Tiantian Zhao / Gregory A Wasney / Patrick Budylowski / Furkan Guvenc / Jocelyn C Newton / Taylor Sicard / Anthony ...Authors: Edurne Rujas / Iga Kucharska / Yong Zi Tan / Samir Benlekbir / Hong Cui / Tiantian Zhao / Gregory A Wasney / Patrick Budylowski / Furkan Guvenc / Jocelyn C Newton / Taylor Sicard / Anthony Semesi / Krithika Muthuraman / Amy Nouanesengsy / Clare Burn Aschner / Katherine Prieto / Stephanie A Bueler / Sawsan Youssef / Sindy Liao-Chan / Jacob Glanville / Natasha Christie-Holmes / Samira Mubareka / Scott D Gray-Owen / John L Rubinstein / Bebhinn Treanor / Jean-Philippe Julien /
Abstract: SARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a ...SARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a modular subunit to drive oligomerization of antibody fragments and transform antibodies targeting SARS-CoV-2 into exceptionally potent neutralizers. Using this platform, half-maximal inhibitory concentration (IC) values as low as 9 × 10 M are achieved as a result of up to 10,000-fold potency enhancements compared to corresponding IgGs. Combination of three different antibody specificities and the fragment crystallizable (Fc) domain on a single multivalent molecule conferred the ability to overcome viral sequence variability together with outstanding potency and IgG-like bioavailability. The MULTi-specific, multi-Affinity antiBODY (Multabody or MB) platform thus uniquely leverages binding avidity together with multi-specificity to deliver ultrapotent and broad neutralizers against SARS-CoV-2. The modularity of the platform also makes it relevant for rapid evaluation against other infectious diseases of global health importance. Neutralizing antibodies are a promising therapeutic for SARS-CoV-2.
#1: Journal: Biorxiv / Year: 2020
Title: Multivalency transforms SARS-CoV-2 antibodies into broad and ultrapotent neutralizers
Authors: Rujas E / Kucharska I / Tan YZ / Benlekbir S / Cui H / Zhao T / Wasney G / Budylowski P / Guvenc F / Newton JC / Sicard T / Semesi A / Muthuraman K / Nouanesengsy A / Prieto K / Bueler SA / ...Authors: Rujas E / Kucharska I / Tan YZ / Benlekbir S / Cui H / Zhao T / Wasney G / Budylowski P / Guvenc F / Newton JC / Sicard T / Semesi A / Muthuraman K / Nouanesengsy A / Prieto K / Bueler SA / Youssef S / Liao-Chan S / Glanville J / Christie-Holmes N / Mubareka S / Gray-Owen SD / Rubinstein JL / Treanor B / Julien JP
History
DepositionSep 28, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.65
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.65
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22739.png

Downloads & links

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Map

FileDownload / File: emd_22739.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM reconstruction of SARS-CoV-2 Spike in complex with the Fab fragment of neutralizing antibody 80
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 240 pix.
= 360.5 Å		1.5 Å/pix.
x 240 pix.
= 360.5 Å		1.5 Å/pix.
x 240 pix.
= 360.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.50208 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65 / Movie #1: 0.65
Minimum - Maximum-2.2050989 - 5.114033
Average (Standard dev.)-0.0033749538 (±0.16059594)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 360.4999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.50208333333331.50208333333331.5020833333333
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z360.500360.500360.500
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-2.2055.114-0.003

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Supplemental data

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Sample components

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Entire : SARS-CoV-2 Spike in complex with the Fab fragment of neutralizing...

EntireName: SARS-CoV-2 Spike in complex with the Fab fragment of neutralizing antibody 80
Components
  • Complex: SARS-CoV-2 Spike in complex with the Fab fragment of neutralizing antibody 80
    • Complex: Fab fragment of neutralizing antibody 80
      • Protein or peptide: Fab 80 heavy chain
      • Protein or peptide: Fab 80 light chain
    • Complex: SARS-CoV-2 Spike
      • Protein or peptide: SARS-CoV-2 Spike

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Supramolecule #1: SARS-CoV-2 Spike in complex with the Fab fragment of neutralizing...

SupramoleculeName: SARS-CoV-2 Spike in complex with the Fab fragment of neutralizing antibody 80
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Fab fragment of neutralizing antibody 80

SupramoleculeName: Fab fragment of neutralizing antibody 80 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: SARS-CoV-2 Spike

SupramoleculeName: SARS-CoV-2 Spike / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Fab 80 heavy chain

MacromoleculeName: Fab 80 heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKASGGTFN RYAFSWVRQA PGQGLEWMGG IIPIFGTANY AQKFQGRVTI TADESTSTAY MELSSLRSED TAVYYCARST RELPEVVDWY FDLWGRGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGA ...String:
QVQLVQSGAE VKKPGSSVKV SCKASGGTFN RYAFSWVRQA PGQGLEWMGG IIPIFGTANY AQKFQGRVTI TADESTSTAY MELSSLRSED TAVYYCARST RELPEVVDWY FDLWGRGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV N HKPSNTKV DKKVEPKSC

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Macromolecule #2: Fab 80 light chain

MacromoleculeName: Fab 80 light chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPDS LAVSLGERAT INCKSSQSVL YSSNNKNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLT ISSLQAEDVA VYYCQQYYSA PLTFGGGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPRE AKVQWKVDNA LQSGNSQESV ...String:
DIVMTQSPDS LAVSLGERAT INCKSSQSVL YSSNNKNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLT ISSLQAEDVA VYYCQQYYSA PLTFGGGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPRE AKVQWKVDNA LQSGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLS SPVTKSFNRG EC

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Macromolecule #3: SARS-CoV-2 Spike

MacromoleculeName: SARS-CoV-2 Spike / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQL PPAYT NSFTRGVYYP DKVFRSSVLH STQDLFLPFF SNVTWFHAIH VSGTN GTKR FDNPVLPFND GVYFASTEKS NIIRGWIFGT TLDSKTQSLL IVNNAT NVV IKVCEFQFCN DPFLGVYYHK NNKSWMESEF RVYSSANNCT ...String:
MFVFLVLLPL VSSQCVNLTT RTQL PPAYT NSFTRGVYYP DKVFRSSVLH STQDLFLPFF SNVTWFHAIH VSGTN GTKR FDNPVLPFND GVYFASTEKS NIIRGWIFGT TLDSKTQSLL IVNNAT NVV IKVCEFQFCN DPFLGVYYHK NNKSWMESEF RVYSSANNCT FEYVSQP FL MDLEGKQGNF KNLREFVFKN IDGYFKIYSK HTPINLVRDL PQGFSALE P LVDLPIGINI TRFQTLLALH RSYLTPGDSS SGWTAGAAAY YVGYLQPRT FLLKYNENGT ITDAVDCALD PLSETKCTLK SFTVEKGIYQ TSNFRVQPTE SIVRFPNIT NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS F STFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADYN YK LPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQ AGSTPC NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA PATV CGPKK STNLVKNKCV NFNFNGLTGT GVLTESNKKF LPFQQFGRDI ADTTD AVRD PQTLEILDIT PCSFGGVSVI TPGTNTSNQV AVLYQDVNCT EVPVAI HAD QLTPTWRVYS TGSNVFQTRA GCLIGAEHVN NSYECDIPIG AGICASY QT QTNSPASVAS QSIIAYTMSL GAENSVAYSN NSIAIPTNFT ISVTTEIL P VSMTKTSVDC TMYICGDSTE CSNLLLQYGS FCTQLNRALT GIAVEQDKN TQEVFAQVKQ IYKTPPIKDF GGFNFSQILP DPSKPSKRSF IEDLLFNKVT LADAGFIKQ YGDCLGDIAA RDLICAQKFN GLTVLPPLLT DEMIAQYTSA L LAGTITSG WTFGAGAALQ IPFAMQMAYR FNGIGVTQNV LYENQKLIAN QF NSAIGKI QDSLSSTASA LGKLQDVVNQ NAQALNTLVK QLSSNFGAIS SVL NDILSR LDPPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAAT KMSEC VLGQSKRVDF CGKGYHLMSF PQSAPHGVVF LHVTYVPAQE KNFTT APAI CHDGKAHFPR EGVFVSNGTH WFVTQRNFYE PQIITTDNTF VSGNCD VVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLGDIS GINASVV NI QKEIDRLNEV AKNLNESLID LQELGKYEQY IKWPSGRLVP RGSPGSGY I PEAPRDGQAY VRKDGEWVLL STFLGHHHHH H

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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

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3TRIS
150.0 mMNaClsodium chloride
0.02 %NaN3sodium azide
GridModel: Homemade / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: glow discharged with PELCO easiGlow (Ted Pella)
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 3610 / Average exposure time: 9.6 sec. / Average electron dose: 45.0 e/Å2
Details: 820 images under 0 degrees tilt, 2790 images under 40 degrees tilt
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4532803
CTF correctionSoftware - Name: cryoSPARC (ver. 2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 7253
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2)

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