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- EMDB-22738: CryoEM reconstruction of SARS-CoV-2 receptor binding domain in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-22738
TitleCryoEM reconstruction of SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46
Map dataFab 46 in complex with RBD domain of SARS-CoV-2 Spike protein.
Sample
  • Complex: SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46
    • Complex: Fab fragment of neutralizing antibody 46
      • Protein or peptide: Fab 46 heavy chain
      • Protein or peptide: Fab 46 light chain
    • Complex: SARS-CoV-2 receptor binding domain
      • Protein or peptide: Receptor Binding Domain of SARS-CoV-2 Spike
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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 J / Semesi A / Muthuraman K / Nouanesengsy A / Prieto K / Bueler S / Youssef S / ...Authors: Rujas E / Kucharska I / Tan YZ / Benlekbir S / Cui H / Zhao T / Wasney G / Budylowski P / Guvenc F / Newton J / Semesi A / Muthuraman K / Nouanesengsy A / Prieto K / Bueler S / 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: 3.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 3.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22738.png

Downloads & links

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Map

FileDownload / File: emd_22738.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFab 46 in complex with RBD domain of SARS-CoV-2 Spike protein.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 200 pix.
= 206. Å		1.03 Å/pix.
x 200 pix.
= 206. Å		1.03 Å/pix.
x 200 pix.
= 206. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.4 / Movie #1: 3.4
Minimum - Maximum-9.889899 - 19.365408
Average (Standard dev.)0.0036772892 (±0.6295338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 206.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z206.000206.000206.000
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-9.89019.3650.004

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Supplemental data

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Sample components

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Entire : SARS-CoV-2 receptor binding domain in complex with the Fab fragme...

EntireName: SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46
Components
  • Complex: SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46
    • Complex: Fab fragment of neutralizing antibody 46
      • Protein or peptide: Fab 46 heavy chain
      • Protein or peptide: Fab 46 light chain
    • Complex: SARS-CoV-2 receptor binding domain
      • Protein or peptide: Receptor Binding Domain of SARS-CoV-2 Spike

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Supramolecule #1: SARS-CoV-2 receptor binding domain in complex with the Fab fragme...

SupramoleculeName: SARS-CoV-2 receptor binding domain in complex with the Fab fragment of neutralizing antibody 46
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Fab fragment of neutralizing antibody 46

SupramoleculeName: Fab fragment of neutralizing antibody 46 / 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 receptor binding domain

SupramoleculeName: SARS-CoV-2 receptor binding domain / 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 46 heavy chain

MacromoleculeName: Fab 46 heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLLESGGG LVQPGRSLRL SCAASGFTFS SYAMSWVRQA PGKGLEWVST IYSGGSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARGD S RDAFDIWG QGTMVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YF PEPVTVS WNSGALTSGV ...String:
EVQLLESGGG LVQPGRSLRL SCAASGFTFS SYAMSWVRQA PGKGLEWVST IYSGGSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCARGD S RDAFDIWG QGTMVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YF PEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YIC NVNHKP SNTKVDKKVE PKSC

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Macromolecule #2: Fab 46 light chain

MacromoleculeName: Fab 46 light chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSIS SWLAWYQQKP GKAPKLLIYD ASNLETGVP SRFSGSGSGT DFTLTISSLQ PEDFATYYCQ QSYSTPFTFG P GTKVDIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KV DNALQSG NSQESVTEQD ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSIS SWLAWYQQKP GKAPKLLIYD ASNLETGVP SRFSGSGSGT DFTLTISSLQ PEDFATYYCQ QSYSTPFTFG P GTKVDIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KV DNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQG LSSPVT KSFNRGEC

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Macromolecule #3: Receptor Binding Domain of SARS-CoV-2 Spike

MacromoleculeName: Receptor Binding Domain of 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: RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC ...String:
RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC YFPLQSYGFQ PTNGVGYQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNFHHHHHH

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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

Concentration2.0 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: 4722 / Average exposure time: 9.6 sec. / Average electron dose: 45.0 e/Å2
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: 3402345
CTF correctionSoftware - Name: cryoSPARC (ver. 2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 32283
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2)

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