9L9T | pdb_00009l9t

Crystal structure of a coronaviral M protein in complex with a C-terminal peptide of the N protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 
    0.291 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 
    0.256 (Depositor) 

Starting Model: experimental
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Literature

Binding of an N protein peptide to M protein of a bat coronavirus.

Wang, X.Yang, S.Yang, P.Sun, Z.Zhou, X.

(2025) J Struct Biol 217: 108234-108234

  • DOI: https://doi.org/10.1016/j.jsb.2025.108234
  • Primary Citation of Related Structures:  
    9L9T

  • PubMed Abstract: 

    The interaction between the membrane (M) protein and the nucleocapsid (N) protein of coronaviruses plays a crucial role in virus assembly and morphogenesis. Previous studies indicate that one M-N interaction occurs between M protein and the carboxy-terminus of N protein. However, the mechanistic details of M-N interactions remain unclear. Here, we present a complex structure of an N protein carboxy-terminal peptide bound to M protein from Pipistrellus bat coronavirus HKU5. The structure shows that the M-N peptide binding site includes a "horizontal" groove located between the carboxy-terminal domain and the transmembrane domain of M protein. Combined with molecular docking and binding analysis, our results provide structural insight into the binding mechanism between M and N proteins of a coronavirus.


  • Organizational Affiliation
    • Department of Integrated Traditional Chinese and Western Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane protein
A, B
220Pipistrellus bat coronavirus HKU5Mutation(s): 0 
Gene Names: M5
UniProt
Find proteins for A3EXD6 (Bat coronavirus HKU5)
Explore A3EXD6 
Go to UniProtKB:  A3EXD6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3EXD6
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N protein peptide poly-Ala model
C, D
5Pipistrellus bat coronavirus HKU5Mutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free:  0.291 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 0.256 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.544α = 90
b = 220.132β = 90
c = 71.097γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770783

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release