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Open data
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Basic information
Entry | Database: PDB / ID: 7zr7 | ||||||||||||
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Title | OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Duyvesteyn, H.M.E. / Ren, J. / Stuart, D.I. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Potent cross-reactive antibodies following Omicron breakthrough in vaccinees. Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / ...Authors: Rungtiwa 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 / ![]() ![]() Abstract: 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. ...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. | ||||||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 733.1 KB | Display | ![]() |
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PDB format | ![]() | 599 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 14885MC ![]() 7zf3C ![]() 7zf4C ![]() 7zf5C ![]() 7zf6C ![]() 7zf7C ![]() 7zf8C ![]() 7zf9C ![]() 7zfaC ![]() 7zfbC ![]() 7zfcC ![]() 7zfdC ![]() 7zfeC ![]() 7zffC ![]() 7zr8C ![]() 7zr9C ![]() 7zrcC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 141993.984 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() Gene: S, 2, wac / Production host: ![]() ![]() #2: Antibody | Mass: 13541.031 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Antibody | Mass: 11286.393 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ![]() Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/1 | ||||||||||||||||||||||||
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: INTEGRATING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 |
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Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Details: Patch CTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106884 / Details: Determined in cryoSPARC / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | B value: 213.7 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 7Q9G Accession code: 7Q9G / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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