8BBN | pdb_00008bbn

SARS-CoV-2 Delta-RBD complexed with BA.2-10 and EY6A Fabs

• PDB DOI: https://doi.org/10.2210/pdb8BBN/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-10-14 Released: 2023-03-22 
• Deposition Author(s): Zhou, D., Ren, J., Stuart, D.I.
• Funding Organization(s): CAMS Innovation Fund for Medical Sciences (CIFMS), Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.58 Å
• R-Value Free: 
  0.314 (Depositor), 0.315 (DCC) 
• R-Value Work: 
  0.265 (Depositor), 0.266 (DCC) 
• R-Value Observed: 
  0.268 (Depositor) 

Starting Model: experimental

Literature

Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.

Dijokaite-Guraliuc, A., Das, R., Zhou, D., Ginn, H.M., Liu, C., Duyvesteyn, H.M.E., Huo, J., Nutalai, R., Supasa, P., Selvaraj, M., de Silva, T.I., Plowright, M., Newman, T.A.H., Hornsby, H., Mentzer, A.J., Skelly, D., Ritter, T.G., Temperton, N., Klenerman, P., Barnes, E., Dunachie, S.J., Roemer, C., Peacock, T.P., Paterson, N.G., Williams, M.A., Hall, D.R., Fry, E.E., Mongkolsapaya, J., Ren, J., Stuart, D.I., Screaton, G.R.

(2023) Cell Rep 42: 112271-112271

• PubMed: 36995936 
• DOI: https://doi.org/10.1016/j.celrep.2023.112271
• Primary Citation Related Structures: 
  8BBN, 8BBO, 8BCZ, 8C3V


• PubMed Abstract: 
  

  In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 and then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional receptor-binding domain (RBD) amino acid substitutions compared with BA.2. We describe a panel of 25 potent monoclonal antibodies (mAbs) generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titer of vaccine or BA.1, BA.2, or BA.4/5 immune serum.

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Organizational Affiliation: 
• Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, 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.
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.
Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK.
Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, 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.
Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, UK.
Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, 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; Department of Medicine, University of Oxford, Oxford, UK.
Biozentrum, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland.
Department of Infectious Disease, Imperial College London, London, UK.
Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK. Electronic address: [e-mail].
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. Electronic address: [e-mail].
Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK. Electronic address: [e-mail].
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: [e-mail].
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. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 356.01 kDa 
• Atom Count: 24,354 
• Modeled Residue Count: 3,171 
• Deposited Residue Count: 3,261 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EY6A Heavy chain	A [auth M], C [auth J], E	226	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EY6A light chain	B [auth N], D [auth K], F	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	G [auth R], J [auth Y], M [auth X]	202	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 3  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BA.2-10 light chain	H [auth L], K [auth D], N [auth B]	214	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
BA.2-10 heavy chain	I [auth H], L [auth C], O [auth A]	230	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.58 Å
• R-Value Free:  0.314 (Depositor), 0.315 (DCC) 
• R-Value Work:  0.265 (Depositor), 0.266 (DCC) 
• R-Value Observed: 0.268 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.655	α = 90
b = 171.691	β = 90
c = 176.991	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Zhou, D., Ren, J., Stuart, D.I.

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Funding Organization	Location	Grant Number
CAMS Innovation Fund for Medical Sciences (CIFMS)	United Kingdom	2018-I2M-2-002
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N00065X/1

Revision History  

• Version 1.0: 2023-03-22
  Type: Initial release
  
• Version 1.1: 2023-04-12
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary