7TN0

SARS-CoV-2 Omicron RBD in complex with human ACE2 and S304 Fab and S309 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement.

McCallum, M.Czudnochowski, N.Rosen, L.E.Zepeda, S.K.Bowen, J.E.Walls, A.C.Hauser, K.Joshi, A.Stewart, C.Dillen, J.R.Powell, A.E.Croll, T.I.Nix, J.Virgin, H.W.Corti, D.Snell, G.Veesler, D.

(2022) Science 375: 864-868

  • DOI: https://doi.org/10.1126/science.abn8652
  • Primary Citation of Related Structures:  
    7TLY, 7TLZ, 7TM0, 7TN0

  • PubMed Abstract: 

    The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or infection with earlier variants due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo-electron microscopy and x-ray crystal structures of the spike protein and the receptor-binding domain bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a blueprint for understanding the marked reduction of binding of other therapeutic mAbs that leads to dampened neutralizing activity. Remodeling of interactions between the Omicron receptor-binding domain and human ACE2 likely explains the enhanced affinity for the host receptor relative to the ancestral virus.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S309 light chain
A, D
214Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S309 heavy chain
B, C
230Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2
E, F
601Homo sapiensMutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1 
Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1
GTEx:  ENSG00000130234 
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UniProt GroupQ9BYF1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
S304 Fab light chainG,
K [auth N]
215Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
S304 Fab heavy chainH,
J [auth M]
223Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1I,
L [auth S]
216Severe acute respiratory syndrome coronavirus 2Mutation(s): 18 
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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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth E]
DB [auth S]
EA [auth E]
GA [auth E]
HA [auth E]
BA [auth E],
DB [auth S],
EA [auth E],
GA [auth E],
HA [auth E],
IA [auth E],
JA [auth F],
LA [auth F],
MA [auth F],
NA [auth F],
RA [auth I]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN
Query on ZN

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AA [auth E],
KA [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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AB [auth S]
M [auth A]
PA [auth G]
QA [auth G]
T [auth B]
AB [auth S],
M [auth A],
PA [auth G],
QA [auth G],
T [auth B],
TA [auth M],
UA [auth M],
VA [auth N],
XA [auth N],
YA [auth N],
ZA [auth S]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

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BB [auth S]
CA [auth E]
CB [auth S]
DA [auth E]
EB [auth S]
BB [auth S],
CA [auth E],
CB [auth S],
DA [auth E],
EB [auth S],
FA [auth E],
N [auth A],
O [auth A],
OA [auth F],
P [auth A],
Q [auth A],
R [auth B],
S [auth B],
SA [auth I],
U [auth C],
V [auth C],
W [auth C],
WA [auth N],
X [auth C],
Y [auth D],
Z [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.28α = 90
b = 183.65β = 95.98
c = 194.55γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2022-02-16
    Changes: Other, Structure summary
  • Version 1.3: 2022-03-09
    Changes: Database references
  • Version 1.4: 2023-10-18
    Changes: Data collection, Refinement description