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 8ASY

SARS-CoV-2 Omicron BA.2.75 RBD in complex with ACE2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A delicate balance between antibody evasion and ACE2 affinity for Omicron BA.2.75.

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

(2022) Cell Rep 42: 111903-111903

  • DOI: https://doi.org/10.1016/j.celrep.2022.111903
  • Primary Citation of Related Structures:  
    8ASY

  • PubMed Abstract: 

    Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have caused successive global waves of infection. These variants, with multiple mutations in the spike protein, are thought to facilitate escape from natural and vaccine-induced immunity and often increase in affinity for ACE2. The latest variant to cause concern is BA.2.75, identified in India where it is now the dominant strain, with evidence of wider dissemination. BA.2.75 is derived from BA.2 and contains four additional mutations in the receptor-binding domain (RBD). Here, we perform an antigenic and biophysical characterization of BA.2.75, revealing an interesting balance between humoral evasion and ACE2 receptor affinity. ACE2 affinity for BA.2.75 is increased 9-fold compared with BA.2; there is also evidence of escape of BA.2.75 from immune serum, particularly that induced by Delta infection, which may explain the rapid spread in India, where where there is a high background of Delta infection. ACE2 affinity appears to be prioritized over greater escape.


  • Organizational Affiliation

    State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK; Guangzhou Laboratory, Bio-island, Guangzhou 510320, China. Electronic address: huojiandong@gird.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Processed angiotensin-converting enzyme 2604Homo sapiensMutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1 
Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1
GTEx:  ENSG00000130234 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYF1
Glycosylation
Glycosylation Sites: 6Go to GlyGen: Q9BYF1-1
Sequence AnnotationsExpand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1219Homo sapiensMutation(s): 17 
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
Sequence AnnotationsExpand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
D [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
R [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]
E [auth A]
K [auth A]
M [auth A]
N [auth A]
C [auth A],
E [auth A],
K [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
S [auth A],
T [auth A],
U [auth B],
V [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.261α = 90
b = 105.261β = 90
c = 220.753γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-02-08
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary