7NEG | pdb_00007neg

Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 Fab

• PDB DOI: https://doi.org/10.2210/pdb7NEG/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-02-04 Released: 2021-03-03 
• Deposition Author(s): Zhou, D., Ren, J., Stuart, D.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), CAMS Innovation Fund for Medical Sciences (CIFMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.223 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera.

Supasa, P., Zhou, D., Dejnirattisai, W., Liu, C., Mentzer, A.J., Ginn, H.M., Zhao, Y., Duyvesteyn, H.M.E., Nutalai, R., Tuekprakhon, A., Wang, B., Paesen, G.C., Slon-Campos, J., Lopez-Camacho, C., Hallis, B., Coombes, N., Bewley, K.R., Charlton, S., Walter, T.S., Barnes, E., Dunachie, S.J., Skelly, D., Lumley, S.F., Baker, N., Shaik, I., Humphries, H.E., Godwin, K., Gent, N., Sienkiewicz, A., Dold, C., Levin, R., Dong, T., Pollard, A.J., Knight, J.C., Klenerman, P., Crook, D., Lambe, T., Clutterbuck, E., Bibi, S., Flaxman, A., Bittaye, M., Belij-Rammerstorfer, S., Gilbert, S., Hall, D.R., Williams, M.A., Paterson, N.G., James, W., Carroll, M.W., Fry, E.E., Mongkolsapaya, J., Ren, J., Stuart, D.I., Screaton, G.R.

(2021) Cell 184: 2201

• PubMed: 33743891 
• DOI: https://doi.org/10.1016/j.cell.2021.02.033
• Primary Citation Related Structures: 
  7NEG, 7NEH


• PubMed Abstract: 
  

  SARS-CoV-2 has caused over 2 million deaths in little over a year. Vaccines are being deployed at scale, aiming to generate responses against the virus spike. The scale of the pandemic and error-prone virus replication is leading to the appearance of mutant viruses and potentially escape from antibody responses. Variant B.1.1.7, now dominant in the UK, with increased transmission, harbors 9 amino acid changes in the spike, including N501Y in the ACE2 interacting surface. We examine the ability of B.1.1.7 to evade antibody responses elicited by natural SARS-CoV-2 infection or vaccination. We map the impact of N501Y by structure/function analysis of a large panel of well-characterized monoclonal antibodies. B.1.1.7 is harder to neutralize than parental virus, compromising neutralization by some members of a major class of public antibodies through light-chain contacts with residue 501. However, widespread escape from monoclonal antibodies or antibody responses generated by natural infection or vaccination was not observed.

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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.
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.
Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
National Infection Service, Public Health England (PHE), Porton Down, Salisbury, 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.
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; NIHR Oxford Biomedical Research Centre, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK.
NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
Worthing Hospital, Worthing, UK.
Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
Nuffield Department of Medicine, University of Oxford, Oxford, UK.
Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
Sir William Dunn School of Pathology University of Oxford, Oxford, UK.
Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury, 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; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand. 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; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, 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].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 71.84 kDa 
• Atom Count: 4,945 
• Modeled Residue Count: 614 
• Deposited Residue Count: 647 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody COVOX-269 Fab heavy chain	A [auth H]	222	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody COVOX-269 Fab light chain	B [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface glycoprotein	C [auth E]	210	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth H], J [auth L], L [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth H], G [auth L], H [auth L], I [auth L], K [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.223 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.099	α = 90
b = 84.95	β = 100.634
c = 57.936	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: 2021-03-03 
Deposition Author(s): Zhou, D., Ren, J., Stuart, D.

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

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references
• Version 1.2: 2021-04-28
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary