9L9T | pdb_00009l9t

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

• PDB DOI: https://doi.org/10.2210/pdb9L9T/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Pipistrellus bat coronavirus HKU5
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2024-12-31 Released: 2025-11-05 
• Deposition Author(s): Wang, X., Sun, Z., Zhou, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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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

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

• PubMed: 40664277 
• DOI: https://doi.org/10.1016/j.jsb.2025.108234
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Integrated Traditional Chinese and Western Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
Department of Integrated Traditional Chinese and Western Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.91 kDa 
• Atom Count: 3,159 
• Modeled Residue Count: 395 
• Deposited Residue Count: 450 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane protein	A, B	220	Pipistrellus bat coronavirus HKU5	Mutation(s): 0  Gene Names: M, 5
UniProt
Find proteins for A3EXD6 (Bat coronavirus HKU5) Explore A3EXD6  Go to UniProtKB:  A3EXD6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N protein peptide poly-Ala model	C, D	5	Pipistrellus bat coronavirus HKU5	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N8E	E [auth A], F [auth A]	3,6,9,12,15-PENTAOXATRICOSAN-1-OL C18 H38 O6 MJELOWOAIAAUJT-UHFFFAOYSA-N

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 = 77.544	α = 90
b = 220.132	β = 90
c = 71.097	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Wang, X., Sun, Z., Zhou, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31770783

Revision History  

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