7ZF6 | pdb_00007zf6

Omi-12 Fab

PDB DOI: https://doi.org/10.2210/pdb7ZF6/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-04-01 Released: 2022-06-01
Deposition Author(s): Zhou, D., Huo, J., Ren, J., Stuart, D.I.
Funding Organization(s): CAMS Innovation Fund for Medical Sciences (CIFMS), Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.265 (Depositor), 0.286 (DCC)
R-Value Work:
0.235 (Depositor), 0.259 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.

Nutalai, R., Zhou, D., Tuekprakhon, A., Ginn, H.M., Supasa, P., Liu, C., Huo, J., Mentzer, A.J., Duyvesteyn, H.M.E., Dijokaite-Guraliuc, A., Skelly, D., Ritter, T.G., Amini, A., Bibi, S., Adele, S., Johnson, S.A., Constantinides, B., Webster, H., Temperton, N., Klenerman, P., Barnes, E., Dunachie, S.J., Crook, D., Pollard, A.J., Lambe, T., Goulder, P., Paterson, N.G., Williams, M.A., Hall, D.R., Mongkolsapaya, J., Fry, E.E., Dejnirattisai, W., Ren, J., Stuart, D.I., Screaton, G.R.

(2022) Cell 185: 2116-2131.e18

PubMed: 35662412 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2022.05.014
Primary Citation Related Structures:
7ZF3, 7ZF4, 7ZF5, 7ZF6, 7ZF7, 7ZF8, 7ZF9, 7ZFA, 7ZFB, 7ZFC, 7ZFD, 7ZFE, 7ZFF, 7ZR7, 7ZR8, 7ZR9, 7ZRC

PubMed 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.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.

Organizational Affiliation

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.

Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK.

Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.

Nuffield Department of Medicine, University of Oxford, Oxford, UK.

Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich, Chatham Maritime, Kent ME4 4TB, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.

Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.

Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.

Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.

Peter Medawar Building for Pathogen Research, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK.

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK. Electronic address: dwanwisa@well.ox.ac.uk.

Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK. Electronic address: ren@strubi.ox.ac.uk.

Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK. Electronic address: dave@strubi.ox.ac.uk.

Macromolecule Content

Total Structure Weight: 49.69 kDa
Atom Count: 3,455
Modeled Residue Count: 436
Deposited Residue Count: 443
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Omi-12 heavy chain	A [auth H]	228	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Omi-12 light chain	B [auth L]	215	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth H] MOL2 format, chain C [auth H] mmCIF format, chain C [auth H]	C [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth H] Interactions & Density Focus chain C [auth H]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain H [auth L] MOL2 format, chain H [auth L] mmCIF format, chain H [auth L]	H [auth L]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Interactions & Density Focus chain H [auth L]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain N [auth L] SDF format, chain P [auth L] SDF format, chain Q [auth L] SDF format, chain O [auth L] SDF format, chain M [auth L] SDF format, chain L SDF format, chain I [auth L] MOL2 format, chain E [auth H] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain N [auth L] MOL2 format, chain P [auth L] MOL2 format, chain Q [auth L] MOL2 format, chain O [auth L] MOL2 format, chain M [auth L] MOL2 format, chain L MOL2 format, chain I [auth L] mmCIF format, chain E [auth H] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain N [auth L] mmCIF format, chain P [auth L] mmCIF format, chain Q [auth L] mmCIF format, chain O [auth L] mmCIF format, chain M [auth L] mmCIF format, chain L mmCIF format, chain I [auth L]	E [auth H] I [auth L] J [auth L] K [auth L] L E [auth H], I [auth L], J [auth L], K [auth L], L, M [auth L], N [auth L], O [auth L], P [auth L], Q [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth H] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L] Interactions & Density Focus chain E [auth H] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain G [auth L] SDF format, chain D [auth H] MOL2 format, chain F [auth L] MOL2 format, chain G [auth L] MOL2 format, chain D [auth H] mmCIF format, chain F [auth L] mmCIF format, chain G [auth L] mmCIF format, chain D [auth H]	D [auth H], F [auth L], G [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain F [auth L] Focus chain G [auth L] Interactions & Density Focus chain D [auth H] Focus chain F [auth L] Focus chain G [auth L]