7CN8

Cryo-EM structure of PCoV_GX spike glycoprotein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution.

Zhang, S.Qiao, S.Yu, J.Zeng, J.Shan, S.Tian, L.Lan, J.Zhang, L.Wang, X.

(2021) Nat Commun 12: 1607-1607

  • DOI: https://doi.org/10.1038/s41467-021-21767-3
  • Primary Citation of Related Structures:  
    7CN4, 7CN8

  • PubMed Abstract: 

    In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection. Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. All three receptor-binding domains (RBDs) of these two spike trimers are in the "down" conformation, indicating they are more prone to adopt the receptor-binding inactive state. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. We further identified critical residues in the RBD underlying different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes. These results collectively indicate that tight RBD-ACE2 binding and efficient RBD conformational sampling are required for the evolution of SARS-CoV-2 to gain highly efficient infection.


  • Organizational Affiliation

    The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, 100084, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoprotein
A, B, C
1,295Pangolin coronavirusMutation(s): 0 
UniProt
Find proteins for A0A6G6A2Q2 (Pangolin coronavirus)
Explore A0A6G6A2Q2 
Go to UniProtKB:  A0A6G6A2Q2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6G6A2Q2
Glycosylation
Glycosylation Sites: 20
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth I],
BA [auth K],
CA [auth l],
D [auth E],
DA [auth N],
AA [auth I],
BA [auth K],
CA [auth l],
D [auth E],
DA [auth N],
E [auth F],
EA [auth O],
F [auth J],
FA [auth R],
G [auth L],
GA [auth m],
H [auth M],
HA [auth U],
I [auth P],
IA [auth Y],
J [auth Q],
JA [auth Z],
K [auth S],
L [auth T],
M [auth V],
N [auth W],
O [auth X],
P [auth a],
Q [auth b],
R [auth e],
S [auth f],
T [auth g],
U [auth h],
V [auth i],
W [auth k],
X [auth D],
Y [auth G],
Z [auth H]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EIC
Query on EIC

Download Ideal Coordinates CCD File 
DB [auth B],
NB [auth C],
TA [auth A]
LINOLEIC ACID
C18 H32 O2
OYHQOLUKZRVURQ-HZJYTTRNSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth B]
BB [auth B]
CB [auth B]
EB [auth C]
FB [auth C]
AB [auth B],
BB [auth B],
CB [auth B],
EB [auth C],
FB [auth C],
GB [auth C],
HB [auth C],
IB [auth C],
JB [auth C],
KA [auth A],
KB [auth C],
LA [auth A],
LB [auth C],
MA [auth A],
MB [auth C],
NA [auth A],
OA [auth A],
PA [auth A],
QA [auth A],
RA [auth A],
SA [auth A],
UA [auth B],
VA [auth B],
WA [auth B],
XA [auth B],
YA [auth B],
ZA [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary