6CJ6 | pdb_00006cj6

Structure of the poxvirus protein F9

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.269 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.226 (Depositor) 
  • R-Value Observed: 
    0.228 (Depositor) 

wwPDB Validation 3D Report Full Report

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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 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. Ulrike.Diesterbeck@gmail.com.

Macromolecule Content 

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

Macromolecules

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|  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
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Reference Sequence

Small Molecules

Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P33

Query on P33


Download:Ideal Coordinates CCD File
TC [auth C]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
P6G

Query on P6G


Download:Ideal Coordinates CCD File
KE [auth D],
LE [auth D],
ME [auth D]		HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
ETE

Query on ETE


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.226 (Depositor) 
  • R-Value Observed: 0.228 (Depositor) 
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