8R80

SARS-CoV-2 Delta RBD in complex with XBB-9 Fab and an anti-Fab nanobody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.03 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.271 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.

Liu, C.Zhou, D.Dijokaite-Guraliuc, A.Supasa, P.Duyvesteyn, H.M.E.Ginn, H.M.Selvaraj, M.Mentzer, A.J.Das, R.de Silva, T.I.Ritter, T.G.Plowright, M.Newman, T.A.H.Stafford, L.Kronsteiner, B.Temperton, N.Lui, Y.Fellermeyer, M.Goulder, P.Klenerman, P.Dunachie, S.J.Barton, M.I.Kutuzov, M.A.Dushek, O.Fry, E.E.Mongkolsapaya, J.Ren, J.Stuart, D.I.Screaton, G.R.

(2024) Cell Rep Med 5: 101553-101553

  • DOI: https://doi.org/10.1016/j.xcrm.2024.101553
  • Primary Citation of Related Structures:  
    8QRF, 8QRG, 8QSQ, 8QTD, 8R80, 8R8K

  • PubMed Abstract: 

    BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
XBB-9 Fab heavy chainA [auth H],
G [auth A]
224Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
XBB-9 Fab light chainB [auth L],
H [auth B]
214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1C [auth E],
D [auth R]
202Severe acute respiratory syndrome coronavirus 2Mutation(s): 2 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
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UniProt GroupP0DTC2
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
anti-Fab nanobodyE [auth N],
F [auth J]
135synthetic constructMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.03 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.271 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.538α = 90
b = 126.398β = 90
c = 164.824γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CAMS Innovation Fund for Medical Sciences (CIFMS)United Kingdom2018-I2M-2-002
Medical Research Council (MRC, United Kingdom)United KingdomMR/N00065X/1
Wellcome TrustUnited Kingdom090532/Z/09/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references
  • Version 1.2: 2024-06-05
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Structure summary