8GP6 | pdb_00008gp6

Structure of the vaccinia virus A16/G9 sub-complex from the orthopoxvirus entry-fusion complex

• PDB DOI: https://doi.org/10.2210/pdb8GP6/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Vaccinia virus WR
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): No 


• Deposited: 2022-08-25 Released: 2023-05-17 
• Deposition Author(s): Lu, G.W., Yang, F.L., Lin, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.273 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: in silico

Literature

Structural basis of poxvirus A16/G9 binding for sub-complex formation.

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

(2023) Emerg Microbes Infect 12: 2179351-2179351

• PubMed: 36757688 
• DOI: https://doi.org/10.1080/22221751.2023.2179351
• Primary Citation Related Structures: 
  8GP6

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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: 77.9 kDa 
• Atom Count: 4,462 
• Modeled Residue Count: 546 
• Deposited Residue Count: 675 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myristoylated protein G9	A [auth B]	327	Vaccinia virus WR	Mutation(s): 0  Gene Names: VACWR087, G9R
UniProt
Find proteins for P07611 (Vaccinia virus (strain Western Reserve)) Explore P07611  Go to UniProtKB:  P07611

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Virion membrane protein A16	B [auth A]	348	Vaccinia virus WR	Mutation(s): 0  Gene Names: VACWR136, A16L
UniProt
Find proteins for P16710 (Vaccinia virus (strain Western Reserve)) Explore P16710  Go to UniProtKB:  P16710

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.273 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.275	α = 90
b = 122.008	β = 90
c = 123.909	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Lu, G.W., Yang, F.L., Lin, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary