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Structure paper

TitlePotent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Journal, issue, pagesCell, Vol. 185, Issue 12, Page 2116-2131.e18, Year 2022
Publish dateJun 9, 2022
AuthorsRungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / Donal Skelly / Thomas G Ritter / Ali Amini / Sagida Bibi / Sandra Adele / Sile Ann Johnson / Bede Constantinides / Hermione Webster / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / Derrick Crook / Andrew J Pollard / Teresa Lambe / Philip Goulder / / Neil G Paterson / Mark A Williams / David R Hall / Juthathip Mongkolsapaya / Elizabeth E Fry / Wanwisa Dejnirattisai / Jingshan Ren / David I Stuart / Gavin R Screaton /
PubMed AbstractHighly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA. ...Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
External linksCell / PubMed:35662412 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.21 - 5.32 Å
Structure data

14885

7zr7

EMDB-14885, PDB-7zr7:
OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
Method: EM (single particle) / Resolution: 3.7 Å

14886

7zr8

EMDB-14886, PDB-7zr8:
OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE RBD (local refinement)
Method: EM (single particle) / Resolution: 3.7 Å

14887

7zr9

EMDB-14887, PDB-7zr9:
OMI-2 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
Method: EM (single particle) / Resolution: 4.0 Å

14910

7zrc

EMDB-14910, PDB-7zrc:
OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE
Method: EM (single particle) / Resolution: 3.5 Å

PDB-7zf3:
SARS-CoV-2 Omicron RBD in complex with Omi-3 and EY6A Fabs
Method: X-RAY DIFFRACTION / Resolution: 3.15 Å

PDB-7zf4:
SARS-CoV-2 Omicron RBD in complex with Omi-9 Fab and nanobody F2
Method: X-RAY DIFFRACTION / Resolution: 4.18 Å

PDB-7zf5:
SARS-CoV-2 Omicron RBD in complex with Omi-12 and Beta-54 Fabs
Method: X-RAY DIFFRACTION / Resolution: 5.32 Å

PDB-7zf6:
Omi-12 Fab
Method: X-RAY DIFFRACTION / Resolution: 2.21 Å

PDB-7zf7:
SARS-CoV-2 Omicron BA.2 RBD in complex with ACE2
Method: X-RAY DIFFRACTION / Resolution: 3.46 Å

PDB-7zf8:
SARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab
Method: X-RAY DIFFRACTION / Resolution: 2.95 Å

PDB-7zf9:
SARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab (P21)
Method: X-RAY DIFFRACTION / Resolution: 3.25 Å

PDB-7zfa:
SARS-CoV-2 Omicron RBD in complex with Omi-6 and COVOX-150 Fabs
Method: X-RAY DIFFRACTION / Resolution: 4.24 Å

PDB-7zfb:
SARS-CoV-2 Omicron RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs
Method: X-RAY DIFFRACTION / Resolution: 3.08 Å

PDB-7zfc:
SARS-CoV-2 Beta RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs
Method: X-RAY DIFFRACTION / Resolution: 3.24 Å

PDB-7zfd:
SARS-CoV-2 Omicron RBD in complex with Omi-25 Fab
Method: X-RAY DIFFRACTION / Resolution: 3.39 Å

PDB-7zfe:
SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1
Method: X-RAY DIFFRACTION / Resolution: 3.25 Å

PDB-7zff:
Omi-42 Fab
Method: X-RAY DIFFRACTION / Resolution: 2.32 Å

Chemicals

ChemComp-GOL:
GLYCEROL

ChemComp-IPA:
ISOPROPYL ALCOHOL / alkaloid*YM

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-SO4:
SULFATE ION

ChemComp-CIT:
CITRIC ACID

ChemComp-HOH:
WATER

ChemComp-ZN:
Unknown entry

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
  • tequatrovirus t4
  • enterobacteria phage t4 (virus)
  • lama glama (llama)
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Omicron / RBD / antibody / Fab / Omi-3 / EY6A / VIRAL PROTEIN/IMMUNE SYSTEM / BA.1 / BA.2 / Omi-12 / Beta-54 / IMMUNE SYSTEM / receptor / ACE2 / COVOX-150 / Omi-6 / Omi-18 / Omi-31 / Beta / Omi-25 / VIRALPROTEIN/IMMUNE SYSTEM / Omi-32 / Omi-42 / STRUCTURAL PROTEIN / SARS-COV2 / SPIKE / GLYCOPROTEIN / B.1.135 / BETA VARIANT / COMPLEX / NEUTRALISING / CONVALESCENT SERA / IMMUNE SYSTEM COMPLEX

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