7DF4

SARS-CoV-2 S-ACE2 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM.

Xu, C.Wang, Y.Liu, C.Zhang, C.Han, W.Hong, X.Wang, Y.Hong, Q.Wang, S.Zhao, Q.Wang, Y.Yang, Y.Chen, K.Zheng, W.Kong, L.Wang, F.Zuo, Q.Huang, Z.Cong, Y.

(2021) Sci Adv 7

  • DOI: 10.1126/sciadv.abe5575
  • Primary Citation of Related Structures:  
    7DF3, 7DF4, 7DK3

  • PubMed Abstract: 
  • The recent outbreaks and rapid international spread of SARS-CoV-2 pose a global health emergency. Its trimeric spike (S) glycoprotein interacts with human ACE2-receptor to mediate viral entry into host-cells. Here we present cryo-EM structures of a tightly closed SARS-CoV-2 S-trimer with packed fusion peptide, and an ACE2-bound S-trimer at 2 ...

    The recent outbreaks and rapid international spread of SARS-CoV-2 pose a global health emergency. Its trimeric spike (S) glycoprotein interacts with human ACE2-receptor to mediate viral entry into host-cells. Here we present cryo-EM structures of a tightly closed SARS-CoV-2 S-trimer with packed fusion peptide, and an ACE2-bound S-trimer at 2.7 Å and 3.8 Å resolution, respectively. Accompanying ACE2 binding to the up receptor-binding domain (RBD), the associated ACE2-RBD exhibits continuous swing-motions within the S-trimer. Noteworthy, SARS-CoV-2 S-trimer appears much more sensitive to ACE2-receptor than SARS-CoV S-trimer regarding receptor-triggered transformation from the closed prefusion state to fusion-prone open state, potentially contributing to the superior infectivity of SARS-CoV-2. We defined the RBD T470-T478 loop and Y505 as viral determinants for specific recognition of SARS-CoV-2 RBD by ACE2. Our findings depict the mechanism of ACE2-induced S-trimer conformational transitions from ground prefusion state toward postfusion state, facilitating development of anti-SARS-CoV-2 vaccines and therapeutics.


    Organizational Affiliation

    Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2A625Homo sapiensMutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1 
Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinC [auth B], B [auth C], D1261Severe acute respiratory syndrome coronavirus 2Mutation(s): 5 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H, I, J, K, L
E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C] , AB [auth D] , BA [auth C] , BB [auth D] , CA [auth C] , CB [auth D] , DA [auth C] , DB [auth D] , 
AA [auth C],  AB [auth D],  BA [auth C],  BB [auth D],  CA [auth C],  CB [auth D],  DA [auth C],  DB [auth D],  EA [auth C],  EB [auth D],  FA [auth C],  FB [auth D],  GA [auth C],  HA [auth B],  IA [auth B],  JA [auth B],  KA [auth B],  LA [auth B],  MA [auth B],  NA [auth B],  OA [auth B],  PA [auth B],  QA [auth B],  RA [auth B],  SA [auth B],  TA [auth D],  UA [auth D],  VA [auth D],  W [auth C],  WA [auth D],  X [auth C],  XA [auth D],  Y [auth C],  YA [auth D],  Z [auth C],  ZA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-11-06 
  • Released Date: 2020-12-16 
  • Deposition Author(s): Cong, X., Yao, C.

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references