7XIV | pdb_00007xiv

Structural insight into the interactions between Lloviu virus VP30 and nucleoprotein

• PDB DOI: https://doi.org/10.2210/pdb7XIV/pdb

• Classification: VIRUS
• Organism(s): Cuevavirus lloviuense
• Expression System: Expression vector pET-mod
• Mutation(s): No 


• Deposited: 2022-04-14 Released: 2022-06-29 
• Deposition Author(s): Dong, S.S., Qin, X.C., Sun, W.Y., Luan, F.C., Wang, J.J., Ma, L., Li, X.X., Yang, G.X., Hao, C.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.269 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the interactions between lloviu virus VP30 and nucleoprotein.

Sun, W., Luan, F., Wang, J., Ma, L., Li, X., Yang, G., Hao, C., Qin, X., Dong, S.

(2022) Biochem Biophys Res Commun 616: 82-88

• PubMed: 35649303 
• DOI: https://doi.org/10.1016/j.bbrc.2022.05.059
• Primary Citation Related Structures: 
  7XIV


• PubMed Abstract: 
  

  The family Filoviridae comprises many notorious viruses, such as Ebola virus (EBOV) and Marburg virus (MARV), that can infect humans and nonhuman primates. Lloviu virus (LLOV), a less well studied filovirus, is considered a potential pathogen for humans. The VP30 C-terminal domain (CTD) of these filoviruses exhibits nucleoprotein (NP) binding and plays an essential role in viral transcription, replication and assembly. In this study, we confirmed the interactions between LLOV VP30 CTD and its NP fragment, and also determined the crystal structure of the chimeric dimeric LLOV NP-VP30 CTD at 2.50 Å resolution. The structure is highly conserved across the family Filoviridae. While in the dimer structure, only one VP30 CTD binds the NP fragment, which indicates that the interaction between LLOV VP30 CTD and NP is not strong. Our work provides a preliminary model to investigate the interactions between LLOV VP30 and NP and suggests a potential target for anti-filovirus drug development.

---

Organizational Affiliation: 
• School of Biological Science and Technology, University of Jinan, Jinan, China.
School of Chemistry and Chemical Engineering, University of Jinan, Jinan, China.
School of Biological Science and Technology, University of Jinan, Jinan, China; School of Chemistry and Chemical Engineering, University of Jinan, Jinan, China. Electronic address: [e-mail].
School of Biological Science and Technology, University of Jinan, Jinan, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 38.74 kDa 
• Atom Count: 2,034 
• Modeled Residue Count: 259 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleocapsid protein,Minor nucleoprotein VP30	A, B	172	Cuevavirus lloviuense	Mutation(s): 0
UniProt
Find proteins for G8EFI1 (Cuevavirus lloviuense) Explore G8EFI1  Go to UniProtKB:  G8EFI1
Find proteins for G8EFI6 (Cuevavirus lloviuense) Explore G8EFI6  Go to UniProtKB:  G8EFI6
UniProt Groups	G8EFI1G8EFI6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.269 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.251	α = 90
b = 64.251	β = 90
c = 175.795	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Dong, S.S., Qin, X.C., Sun, W.Y., Luan, F.C., Wang, J.J., Ma, L., Li, X.X., Yang, G.X., Hao, C.Y.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32070267,31622007,31670237
Other government	China	National key R&DProgram of China (2018YFD1000501)
Other government	China	Shandong Provincial Natural Science Foundation, China (ZR2019ZD48, ZR2020QC057)
Other government	China	Taishan Scholars Project (tsqn201812079)
Other government	China	Higher Educational Science and Technology Program of Jinan City (2020GXRC058)

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description