6CJ6

Structure of the poxvirus protein F9

• PDB DOI: https://doi.org/10.2210/pdb6CJ6/pdb

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


• Deposited: 2018-02-26 Released: 2019-03-06 
• Deposition Author(s): Diesterbeck, U.S., Gittis, A.G., Garboczi, D.N., Moss, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.269 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 

Literature

The 2.1 angstrom structure of protein F9 and its comparison to L1, two components of the conserved poxvirus entry-fusion complex.

Diesterbeck, U.S., Gittis, A.G., Garboczi, D.N., Moss, B.

(2018) Sci Rep 8: 16807-16807

• PubMed: 30429486 
• DOI: https://doi.org/10.1038/s41598-018-34244-7
• Primary Citation of Related Structures:  
  6CJ6


• PubMed Abstract: 
  

  The poxvirus F9 protein is a component of the vaccinia virus entry fusion complex (EFC) which consists of 11 proteins. The EFC forms a unique apparatus among viral fusion proteins and complexes. We solved the atomic structure of the F9 ectodomain at 2.10 Å. A structural comparison to the ectodomain of the EFC protein L1 indicated a similar fold and organization, in which a bundle of five α-helices is packed against two pairs of β-strands. However, instead of the L1 myristoylation site and hydrophobic cavity, F9 possesses a protruding loop between α-helices α3 and α4 starting at Gly90. Gly90 is conserved in all poxviruses except Salmon gill poxvirus (SGPV) and Diachasmimorpha longicaudata entomopoxvirus. Phylogenetic sequence analysis of all Poxviridae F9 and L1 orthologs revealed the SGPV genome to contain the most distantly related F9 and L1 sequences compared to the vaccinia proteins studied here. The structural differences between F9 and L1 suggest functional adaptations during evolution from a common precursor that underlie the present requirement for each protein.

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Organizational Affiliation: 

Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.22 kDa 
• Atom Count: 6,060 
• Modelled Residue Count: 653 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein F9	A, B, C, D	176	Vaccinia virus WR	Mutation(s): 0  Gene Names: VACWR048, F9L
UniProt
Find proteins for P24361 (Vaccinia virus (strain Western Reserve)) Explore P24361  Go to UniProtKB:  P24361

Small Molecules

Ligands 14 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	TC [auth C]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
P6G	KE [auth D], LE [auth D], ME [auth D]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
ETE	HB [auth B], UC [auth C]	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C9 H20 O5 ZNYRFEPBTVGZDN-UHFFFAOYSA-N
PG4	DB [auth B], DE [auth D], E [auth A], EE [auth D], F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	AE [auth C], BE [auth C], JC [auth B], YF [auth D], ZD [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PG0	EB [auth B], FE [auth D], G [auth A], GE [auth D], H [auth A], I [auth A], J [auth A], NC [auth C], OC [auth C]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
PEG	FB [auth B], GB [auth B], HE [auth D], IE [auth D], JE [auth D], K [auth A], L [auth A], PC [auth C], QC [auth C], RC [auth C], SC [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	CD [auth C], DD [auth C], ED [auth C], FD [auth C], V [auth A], YE [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ETX	AG [auth D], BB [auth A], CB [auth A], CE [auth C], KC [auth B], LC [auth B], MC [auth B], ZF [auth D]	2-ETHOXYETHANOL C4 H10 O2 ZNQVEEAIQZEUHB-UHFFFAOYSA-N
PGO	AB [auth A], GC [auth B], HC [auth B], IC [auth B], VF [auth D], WF [auth D], XF [auth D], YA [auth A], YD [auth C], ZA [auth A]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
PDO	AA [auth A], AF [auth D], BA [auth A], CA [auth A], GD [auth C], HD [auth C], OB [auth B], PB [auth B], QB [auth B], W [auth A], X [auth A], Y [auth A], Z [auth A], ZE [auth D]	1,3-PROPANDIOL C3 H8 O2 YPFDHNVEDLHUCE-UHFFFAOYSA-N
EDO	AD [auth C], BD [auth C], IB [auth B], JB [auth B], KB [auth B], LB [auth B], M [auth A], MB [auth B], N [auth A], NB [auth B], NE [auth D], O [auth A], OE [auth D], P [auth A], PE [auth D], Q [auth A], QE [auth D], R [auth A], RE [auth D], S [auth A], SE [auth D], T [auth A], TE [auth D], U [auth A], UE [auth D], VC [auth C], VE [auth D], WC [auth C], WE [auth D], XC [auth C], XE [auth D], YC [auth C], ZC [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
EOH	AC [auth B], BC [auth B], BF [auth D], CC [auth B], CF [auth D], DA [auth A], DF [auth D], EA [auth A], EF [auth D], FA [auth A], FF [auth D], GA [auth A], GF [auth D], HA [auth A], HF [auth D], IA [auth A], ID [auth C], IF [auth D], JA [auth A], JD [auth C], JF [auth D], KA [auth A], KD [auth C], KF [auth D], LA [auth A], LD [auth C], LF [auth D], MA [auth A], MD [auth C], MF [auth D], NA [auth A], ND [auth C], OA [auth A], OD [auth C], PA [auth A], PD [auth C], QD [auth C], RB [auth B], RD [auth C], SB [auth B], TB [auth B], UB [auth B], VB [auth B], WB [auth B], XB [auth B], YB [auth B], ZB [auth B]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
MOH	DC [auth B], EC [auth B], FC [auth B], NF [auth D], OF [auth D], PF [auth D], QA [auth A], QF [auth D], RA [auth A], RF [auth D], SA [auth A], SD [auth C], SF [auth D], TA [auth A], TD [auth C], TF [auth D], UA [auth A], UD [auth C], UF [auth D], VA [auth A], VD [auth C], WA [auth A], WD [auth C], XA [auth A], XD [auth C]	METHANOL C H4 O OKKJLVBELUTLKV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.269 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.45	α = 90
b = 75.08	β = 90
c = 136.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-06 
Deposition Author(s): Diesterbeck, U.S., Gittis, A.G., Garboczi, D.N., Moss, B.

Revision History  

• Version 1.0: 2019-03-06
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary