7XPG | pdb_00007xpg

Cryo-EM structure of the T=3 lake sinai virus 1 (delta-N48) virus-like capsid at pH 6.5

• PDB DOI: https://doi.org/10.2210/pdb7XPG/pdb
• NAKB: 7XPG
• EM Map EMD-33373: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Sinaivirus apis, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-05-04 Released: 2023-02-08 
• Deposition Author(s): Chen, N.C., Wang, C.H., Chen, C.J., Yoshimura, M., Guan, H.H., Chuankhayan, P., Lin, C.C.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.51 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions.

Chen, N.C., Wang, C.H., Yoshimura, M., Yeh, Y.Q., Guan, H.H., Chuankhayan, P., Lin, C.C., Lin, P.J., Huang, Y.C., Wakatsuki, S., Ho, M.C., Chen, C.J.

(2023) Nat Commun 14: 545-545

• PubMed: 36726015 
• DOI: https://doi.org/10.1038/s41467-023-36235-3
• Primary Citation Related Structures: 
  7XPA, 7XPB, 7XPD, 7XPE, 7XPF, 7XPG


• PubMed Abstract: 
  

  Understanding the structural diversity of honeybee-infecting viruses is critical to maintain pollinator health and manage the spread of diseases in ecology and agriculture. We determine cryo-EM structures of T = 4 and T = 3 capsids of virus-like particles (VLPs) of Lake Sinai virus (LSV) 2 and delta-N48 LSV1, belonging to tetraviruses, at resolutions of 2.3-2.6 Å in various pH environments. Structural analysis shows that the LSV2 capsid protein (CP) structural features, particularly the protruding domain and C-arm, differ from those of other tetraviruses. The anchor loop on the central β-barrel domain interacts with the neighboring subunit to stabilize homo-trimeric capsomeres during assembly. Delta-N48 LSV1 CP interacts with ssRNA via the rigid helix α1', α1'-α1 loop, β-barrel domain, and C-arm. Cryo-EM reconstructions, combined with X-ray crystallographic and small-angle scattering analyses, indicate that pH affects capsid conformations by regulating reversible dynamic particle motions and sizes of LSV2 VLPs. C-arms exist in all LSV2 and delta-N48 LSV1 VLPs across varied pH conditions, indicating that autoproteolysis cleavage is not required for LSV maturation. The observed linear domino-scaffold structures of various lengths, made up of trapezoid-shape capsomeres, provide a basis for icosahedral T = 4 and T = 3 architecture assemblies. These findings advance understanding of honeybee-infecting viruses that can cause Colony Collapse Disorder.

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Organizational Affiliation: 
• Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan, ROC.
Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan, ROC.
Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30043, Taiwan, ROC.
Department of Structural Biology, Stanford University, Stanford, CA, 94305, USA.
SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Structural Molecular Biology, Menlo Park, CA, 94025, USA.
Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan, ROC. [e-mail].
Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan, ROC. [e-mail].
Department of Physics, National Tsing Hua University, Hsinchu, 30043, Taiwan, ROC. [e-mail].
Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, ROC. [e-mail].
Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC. [e-mail].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 180-mer - A180 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 190.76 kDa 
• Atom Count: 10,935 
• Modeled Residue Count: 1,395 
• Deposited Residue Count: 1,701 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein alpha	A, B, C	565	Sinaivirus apis	Mutation(s): 0
UniProt
Find proteins for A0A223DNC8 (Sinaivirus apis) Explore A0A223DNC8  Go to UniProtKB:  A0A223DNC8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*G)-3')	D, E, F	2	Escherichia coli

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.51 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-08 
Deposition Author(s): Chen, N.C., Wang, C.H., Chen, C.J., Yoshimura, M., Guan, H.H., Chuankhayan, P., Lin, C.C.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2023-02-08
  Type: Initial release
  
• Version 1.1: 2023-02-15
  Changes: Database references
• Version 1.2: 2023-08-16
  Changes: Data collection
• Version 1.3: 2024-05-08
  Changes: Database references