8WHZ | pdb_00008whz

BA.2.86 RBD in complex with hACE2 (local refinement)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8WHZ

This is version 1.3 of the entry. See complete history

Literature

Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity.

Liu, P.Yue, C.Meng, B.Xiao, T.Yang, S.Liu, S.Jian, F.Zhu, Q.Yu, Y.Ren, Y.Wang, P.Li, Y.Wang, J.Mao, X.Shao, F.Wang, Y.Gupta, R.K.Cao, Y.Wang, X.

(2024) Natl Sci Rev 11: nwae206-nwae206

  • DOI: https://doi.org/10.1093/nsr/nwae206
  • Primary Citation Related Structures: 
    8WHS, 8WHU, 8WHV, 8WHW, 8WHZ, 8X4H, 8X4Z, 8X50, 8X55, 8X56, 8X5Q, 8X5R, 8XUR, 8XUS, 8XUT, 8XUU

  • PubMed Abstract: 

    Selective pressures have given rise to a number of SARS-CoV-2 variants during the prolonged course of the COVID-19 pandemic. Recently evolved variants differ from ancestors in additional glycosylation within the spike protein receptor-binding domain (RBD). Details of how the acquisition of glycosylation impacts viral fitness and human adaptation are not clearly understood. Here, we dissected the role of N354-linked glycosylation, acquired by BA.2.86 sub-lineages, as a RBD conformational control element in attenuating viral infectivity. The reduced infectivity is recovered in the presence of heparin sulfate, which targets the 'N354 pocket' to ease restrictions of conformational transition resulting in a 'RBD-up' state, thereby conferring an adjustable infectivity. Furthermore, N354 glycosylation improved spike cleavage and cell-cell fusion, and in particular escaped one subset of ADCC antibodies. Together with reduced immunogenicity in hybrid immunity background, these indicate a single spike amino acid glycosylation event provides selective advantage in humans through multiple mechanisms.


  • Organizational Affiliation
    • CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecule Content 

  • Total Structure Weight: 92.64 kDa 
  • Atom Count: 6,515 
  • Modeled Residue Count: 791 
  • Deposited Residue Count: 791 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Processed angiotensin-converting enzyme 2597Homo 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: 4Go to GlyGen: Q9BYF1-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S1194Severe acute respiratory syndrome coronavirus 2Mutation(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
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



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

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2024-08-21
    Changes: Data collection, Database references
  • Version 1.3: 2024-11-06
    Changes: Data collection, Structure summary