6CJ6

Structure of the poxvirus protein F9

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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA. [email protected].


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein F9
A, B, C, D
176Vaccinia virus WRMutation(s): 0 
Gene Names: VACWR048, F9L
UniProt
Find proteins for P24361 (Vaccinia virus (strain Western Reserve))
Explore P24361 
Go to UniProtKB:  P24361
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24361
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33
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TC [auth C]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
P6G
Query on P6G
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KE [auth D],
LE [auth D],
ME [auth D]		HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
ETE
Query on ETE
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HB [auth B],
UC [auth C]		2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C9 H20 O5
ZNYRFEPBTVGZDN-UHFFFAOYSA-N
PG4
Query on PG4
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DB [auth B],
DE [auth D],
E [auth A],
EE [auth D],
F [auth A]		TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE
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AE [auth C],
BE [auth C],
JC [auth B],
YF [auth D],
ZD [auth C]		TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PG0
Query on PG0
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EB [auth B]
FE [auth D]
G [auth A]
GE [auth D]
H [auth A]
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
Query on PEG
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FB [auth B]
GB [auth B]
HE [auth D]
IE [auth D]
JE [auth D]
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
Query on GOL
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CD [auth C]
DD [auth C]
ED [auth C]
FD [auth C]
V [auth A]
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
Query on ETX
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AG [auth D]
BB [auth A]
CB [auth A]
CE [auth C]
KC [auth B]
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
Query on PGO
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AB [auth A]
GC [auth B]
HC [auth B]
IC [auth B]
VF [auth D]
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
Query on PDO
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AA [auth A]
AF [auth D]
BA [auth A]
CA [auth A]
GD [auth C]
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
Query on EDO
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AD [auth C]
BD [auth C]
IB [auth B]
JB [auth B]
KB [auth B]
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
Query on EOH
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AC [auth B]
BC [auth B]
BF [auth D]
CC [auth B]
CF [auth D]
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
Query on MOH
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DC [auth B]
EC [auth B]
FC [auth B]
NF [auth D]
OF [auth D]
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 = 65.45α = 90
b = 75.08β = 90
c = 136.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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