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 

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Ligand Structure Quality Assessment 


This is version 1.3 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: 10.1126/science.abn8652
  • Primary Citation of Related Structures:  
    7TLY, 7TLZ, 7TM0, 7TN0

  • PubMed Abstract: 
  • The 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 ...

    The 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

    Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
S309 light chainA, D214Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
S309 heavy chainB, C230Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2E, F601Homo sapiensMutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
EC: 3.4.17.23 (UniProt), 3.4.17 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
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PHAROS:  Q9BYF1
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UniProt GroupQ9BYF1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
S304 Fab light chainG,
K [auth N]
215Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
S304 Fab heavy chainH,
J [auth M]
223Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence 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)
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UniProt GroupP0DTC2
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Small Molecules
Ligands 4 Unique
IDChainsName / 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
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth E],
KA [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
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

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Ligand Structure Quality Assessment 



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