9MAO | pdb_00009mao

SARS-CoV-2 spike-Crp5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation

Currently 9MAO does not have a validation slider image.


This is version 1.0 of the entry. See complete history

Literature

Enteric alpha-defensins contribute to intestinal mucosal immunity against SARS-CoV-2 infection.

Yang, Y.Yang, Q.Huang, X.Liao, C.Chen, Z.Lu, W.

(2026) Mucosal Immunol : 100392-100392

  • DOI: https://doi.org/10.1016/j.mucimm.2026.100392
  • Primary Citation Related Structures: 
    9MAO, 9VFX

  • PubMed Abstract: 

    SARS-CoV-2 primarily targets epithelial cells in the respiratory and intestinal tracts where its cognate receptor ACE2 and obligate processing enzymes furin and TMPRSS2 are richly expressed. However, compared with severe inflammation and tissue damage in the lungs of a COVID-19 patient, clinical lesions in the intestine are rare, suggesting an effective intestinal mucosal immunity against SARS-CoV-2 infection. Here, we report that MMP7 -/- /hACE2 hybrid mice lacking mature enteric α-defensins or cryptdins were more susceptible to SARS-CoV-2 infection in the intestine than K18-hACE2 transgenic mice. The mouse α-defensin cryptdin-5 (Crp5) displayed potent and broad antiviral activity in vitro and in vivo by two distinct mechanisms, (1) directly targeting the RBD of the spike (S) protein to antagonize its interactions with ACE2, thus blocking viral attachment, membrane fusion and cell-to-cell transmission, and (2) binding to the 630 loop of the S protein to induce its multimerization, thereby impairing proteolytic processing, membrane fusion and, ultimately, viral infectivity. Our findings imply that enteric α-defensins help alleviate, as host protective factors, Covid-19 symptoms in the intestine despite higher ACE2 expression in the gut than in the lungs, and that Crp5 may be developed as a broad-spectrum antiviral for the treatment of coronavirus infection irrespective of virus type and variant.


  • Organizational Affiliation
    • Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, Shanghai 200032, China.

Macromolecule Content 

  • Total Structure Weight: 436.83 kDa 
  • Atom Count: 24,741 
  • Modeled Residue Count: 3,130 
  • Deposited Residue Count: 3,855 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoproteinA [auth C],
B,
C [auth A]
1,273Severe acute respiratory syndrome coronavirus 2Mutation(s): 6 
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: 12Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-defensin 536Mus musculusMutation(s): 0 
UniProt
Find proteins for P28312 (Mus musculus)
Explore P28312 
Go to UniProtKB:  P28312
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28312
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG(
Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
E [auth C]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
E [auth C],
EA [auth B],
F [auth C],
FA [auth A],
G [auth C],
GA [auth A],
H [auth C],
HA [auth A],
I [auth C],
IA [auth A],
J [auth C],
JA [auth A],
K [auth C],
KA [auth A],
L [auth C],
LA [auth A],
M [auth C],
MA [auth A],
N [auth C],
NA [auth A],
O [auth C],
OA [auth A],
P [auth C],
PA [auth A],
Q [auth C],
QA [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [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: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1_3660

Structure Validation

Currently 9MAO does not have a validation slider image.



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31970146
National Natural Science Foundation of China (NSFC)China82030062

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release