7WP9 | pdb_00007wp9

SARS-CoV-2 Omicron Variant SPIKE trimer, all RBDs down


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7WP9

This is version 1.2 of the entry. See complete history

Literature

Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody.

Yin, W.Xu, Y.Xu, P.Cao, X.Wu, C.Gu, C.He, X.Wang, X.Huang, S.Yuan, Q.Wu, K.Hu, W.Huang, Z.Liu, J.Wang, Z.Jia, F.Xia, K.Liu, P.Wang, X.Song, B.Zheng, J.Jiang, H.Cheng, X.Jiang, Y.Deng, S.J.Xu, H.E.

(2022) Science 375: 1048-1053

  • DOI: https://doi.org/10.1126/science.abn8863
  • Primary Citation Related Structures: 
    7WP9, 7WPA, 7WPB, 7WPC, 7WPD, 7WPE, 7WPF, 7WRV

  • PubMed Abstract: 

    The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has become the dominant infective strain. We report the structures of the Omicron spike trimer on its own and in complex with angiotensin-converting enzyme 2 (ACE2) or an anti-Omicron antibody. Most Omicron mutations are located on the surface of the spike protein and change binding epitopes to many current antibodies. In the ACE2-binding site, compensating mutations strengthen receptor binding domain (RBD) binding to ACE2. Both the RBD and the apo form of the Omicron spike trimer are thermodynamically unstable. An unusual RBD-RBD interaction in the ACE2-spike complex supports the open conformation and further reinforces ACE2 binding to the spike trimer. A broad-spectrum therapeutic antibody, JMB2002, which has completed a phase 1 clinical trial, maintains neutralizing activity against Omicron. JMB2002 binds to RBD differently from other characterized antibodies and inhibits ACE2 binding.


  • Organizational Affiliation
    • The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Macromolecule Content 

  • Total Structure Weight: 407.8 kDa 
  • Atom Count: 25,077 
  • Modeled Residue Count: 3,141 
  • Deposited Residue Count: 3,615 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,205Severe acute respiratory syndrome coronavirus 2Mutation(s): 35 
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: 7Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F, G, H
D, E, F, G, H, I, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
K [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth B]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81902085
National Natural Science Foundation of China (NSFC)China32130022

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary