7YTU | pdb_00007ytu

Crystal structure of vaccinia virus G3/L5 sub-complex (SeMet-labeled, P31 space group)

• PDB DOI: https://doi.org/10.2210/pdb7YTU/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Vaccinia virus WR
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-08-16 Released: 2023-02-08 
• Deposition Author(s): Lin, S., Yue, D., Lu, G.W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal structure of vaccinia virus G3/L5 sub-complex reveals a novel fold with extended inter-molecule interactions conserved among orthopoxviruses.

Lin, S., Yue, D., Yang, F., Chen, Z., He, B., Cao, Y., Dong, H., Li, J., Zhao, Q., Lu, G.

(2023) Emerg Microbes Infect 12: e2160661-e2160661

• PubMed: 36533407 
• DOI: https://doi.org/10.1080/22221751.2022.2160661
• Primary Citation of Related Structures:  
  7YTT, 7YTU

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Organizational Affiliation: 
• West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, People's Republic of China.
Disaster Medicine Center, West China Hospital, Sichuan University, Chengdu, People's Republic of China.
Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, People's Republic of China.
School of Basic Medical Sciences, Chengdu University, Chengdu, People's Republic of China.
College of Food and Biological Engineering, Chengdu University, Chengdu, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.77 kDa 
• Atom Count: 1,149 
• Modeled Residue Count: 131 
• Deposited Residue Count: 171 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein G3	A	92	Vaccinia virus WR	Mutation(s): 0  Gene Names: VACWR079, G3L
UniProt
Find proteins for P68458 (Vaccinia virus (strain Western Reserve)) Explore P68458  Go to UniProtKB:  P68458

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein L5	B	79	Vaccinia virus WR	Mutation(s): 0  Gene Names: VACWR092, L5R
UniProt
Find proteins for P68623 (Vaccinia virus (strain Western Reserve)) Explore P68623  Go to UniProtKB:  P68623

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.039	α = 90
b = 54.039	β = 90
c = 42.742	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELXDE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-08 
Deposition Author(s): Lin, S., Yue, D., Lu, G.W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-02-08
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary