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- EMDB-26389: J08 fragment antigen binding in complex with Omicron SARS-CoV-2-6... -

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Basic information

Entry
Database: EMDB / ID: EMD-26389
TitleJ08 fragment antigen binding in complex with Omicron SARS-CoV-2-6P S protein
Map dataFull map
Sample
  • Complex: J08 fragment antigen binding in complex with Omicron SARS-CoV-2-6P S protein
    • Other: Omicron SARS-CoV-2-6P S protein
    • Other: J08 fragment antigen binding heavy chain variable domain
    • Other: J08 fragment antigen binding light chain variable domain
KeywordsCOVID / SARS / CoV-2 / viral glycoprotein / Spike / stabilizing mutations / coronavirus / ultrapotent antibody / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsOzorowski G / Torres JL / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody.
Authors: Jonathan L Torres / Gabriel Ozorowski / Emanuele Andreano / Hejun Liu / Jeffrey Copps / Giulia Piccini / Lorena Donnici / Matteo Conti / Cyril Planchais / Delphine Planas / Noemi Manganaro / ...Authors: Jonathan L Torres / Gabriel Ozorowski / Emanuele Andreano / Hejun Liu / Jeffrey Copps / Giulia Piccini / Lorena Donnici / Matteo Conti / Cyril Planchais / Delphine Planas / Noemi Manganaro / Elisa Pantano / Ida Paciello / Piero Pileri / Timothée Bruel / Emanuele Montomoli / Hugo Mouquet / Olivier Schwartz / Claudia Sala / Raffaele De Francesco / Ian A Wilson / Rino Rappuoli / Andrew B Ward /
Abstract: As the coronavirus disease 2019 (COVID-19) pandemic continues, there is a strong need for highly potent monoclonal antibodies (mAbs) that are resistant against severe acute respiratory syndrome ...As the coronavirus disease 2019 (COVID-19) pandemic continues, there is a strong need for highly potent monoclonal antibodies (mAbs) that are resistant against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VoCs). Here, we evaluate the potency of the previously described mAb J08 against these variants using cell-based assays and delve into the molecular details of the binding interaction using cryoelectron microscopy (cryo-EM) and X-ray crystallography. We show that mAb J08 has low nanomolar affinity against most VoCs and binds high on the receptor binding domain (RBD) ridge, away from many VoC mutations. These findings further validate the phase II/III human clinical trial underway using mAb J08 as a monoclonal therapy.
History
DepositionMar 9, 2022-
Header (metadata) releaseMay 11, 2022-
Map releaseMay 11, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26389.png

Downloads & links

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Map

FileDownload / File: emd_26389.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 384 pix.
= 437.76 Å		1.14 Å/pix.
x 384 pix.
= 437.76 Å		1.14 Å/pix.
x 384 pix.
= 437.76 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.010687823 - 0.023462422
Average (Standard dev.)0.000018169318 (±0.0010591515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 437.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26389_msk_1.map
Projections & Slices
AxesZYX

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Half map: Half map 1

Fileemd_26389_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_26389_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : J08 fragment antigen binding in complex with Omicron SARS-CoV-2-6...

EntireName: J08 fragment antigen binding in complex with Omicron SARS-CoV-2-6P S protein
Components
  • Complex: J08 fragment antigen binding in complex with Omicron SARS-CoV-2-6P S protein
    • Other: Omicron SARS-CoV-2-6P S protein
    • Other: J08 fragment antigen binding heavy chain variable domain
    • Other: J08 fragment antigen binding light chain variable domain

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Supramolecule #1: J08 fragment antigen binding in complex with Omicron SARS-CoV-2-6...

SupramoleculeName: J08 fragment antigen binding in complex with Omicron SARS-CoV-2-6P S protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Omicron SARS-CoV-2-6P S protein

MacromoleculeName: Omicron SARS-CoV-2-6P S protein / type: other / ID: 1 / Classification: other
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVYF ASIEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD HKNNKSWMES EFRVYSSANN CTFEYVSQPF ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVYF ASIEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD HKNNKSWMES EFRVYSSANN CTFEYVSQPF LMDLEGKQGN FKNLREFVFK NIDGYFKIYS KHTPILVREP EDLPQGFSAL EPLVDLPIGI NITRFQTLLA LHRSYLTPGD SSSGWTAGAA AYYVGYLQPR TFLLKYNENG TITDAVDCAL DPLSETKCTL KSFTVEKGIY QTSNFRVQPT ESIVRFPNIT NLCPFDEVFN ATRFASVYAW NRKRISNCVA DYSVLYNLAP FFTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGNIADYNY KLPDDFTGCV IAWNSNKLDS KVSGNYNYLY RLFRKSNLKP FERDISTEIY QAGNKPCNGV AGFNCYFPLR SYSFRPTYGV GHQPYRVVVL SFELLHAPAT VCGPKKSTNL VKNKCVNFNF NGLKGTGVLT ESNKKFLPFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ GVNCTEVPVA IHADQLTPTW RVYSTGSNVF QTRAGCLIGA EYVNNSYECD IPIGAGICAS YQTQTKSHGS ASSVASQSII AYTMSLGAEN SVAYSNNSIA IPTNFTISVT TEILPVSMTK TSVDCTMYIC GDSTECSNLL LQYGSFCTQL KRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKYFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFKGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGPA LQIPFPMQMA YRFNGIGVTQ NVLYENQKLI ANQFNSAIGK IQDSLSSTPS ALGKLQDVVN HNAQALNTLV KQLSSKFGAI SSVLNDIFSR LDPPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QSAPHGVVFL HVTYVPAQEK NFTTAPAICH DGKAHFPREG VFVSNGTHWF VTQRNFYEPQ IITTDNTFVS GNCDVVIGIV NNTVYDPLQP ELDSFKEELD KYFKNHTSPD VDLGDISGIN ASVVNIQKEI DRLNEVAKNL NESLIDLQEL GKYEQGSGYI PEAPRDGQAY VRKDGEWVLL STFLGRSLEV LFQGPGSAWS HPQFEKGGGS GGGGSGGSAW SHPQFEK
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #2: J08 fragment antigen binding heavy chain variable domain

MacromoleculeName: J08 fragment antigen binding heavy chain variable domain
type: other / ID: 2 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGSSVKV SCKASGGTFS SYTISWVRQA PGQGLEWMGR IIPILDRVMY AQKFQGRVTI TADKSTSTAY MELSSLRSED TAVYYCARRA IDSDTYVEQS HFDYWGQGTL VTVSSAS
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #3: J08 fragment antigen binding light chain variable domain

MacromoleculeName: J08 fragment antigen binding light chain variable domain
type: other / ID: 3 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString:
EIVMTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPSLLIYD ASNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ PLTFGGGTKV EIKRT
Recombinant expressionOrganism: Homo sapiens (human)

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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

Concentration3 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
50.0 mMTris
150.0 mMsodium chloride
0.005 mMlauryl maltose neopentyl glycol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 240000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vxx

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 3808
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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