8QRF | pdb_00008qrf

SARS-CoV-2 delta RBD complexed with XBB-6 and beta-49 Fabs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 
    0.317 (Depositor), 0.318 (DCC) 
  • R-Value Work: 
    0.272 (Depositor), 0.272 (DCC) 
  • R-Value Observed: 
    0.275 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8QRF

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 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.

Macromolecule Content 

  • Total Structure Weight: 117.97 kDa 
  • Atom Count: 8,096 
  • Modeled Residue Count: 1,061 
  • Deposited Residue Count: 1,087 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S1A [auth E]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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-49 light chain216Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-49 heavy chainC [auth A]223Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
XBB-6 heavy chainD [auth H]230Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
XBB-6 light chainE [auth L]216Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth C]4N-Glycosylation
Glycosylation Resources
GlyTouCan: G32152BH
GlyCosmos: G32152BH
GlyGen: G32152BH

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free:  0.317 (Depositor), 0.318 (DCC) 
  • R-Value Work:  0.272 (Depositor), 0.272 (DCC) 
  • R-Value Observed: 0.275 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.106α = 90
b = 146.544β = 90
c = 51.158γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



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

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: 2024-10-09
    Changes: Structure summary