6YFB

Virus-like particle of bacteriophage AVE016


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Three-dimensional structure of 22 uncultured ssRNA bacteriophages: Flexibility of the coat protein fold and variations in particle shapes.

Rumnieks, J.Lieknina, I.Kalnins, G.Sisovs, M.Akopjana, I.Bogans, J.Tars, K.

(2020) Sci Adv 6

  • DOI: 10.1126/sciadv.abc0023
  • Primary Citation of Related Structures:  
    6YF7, 6YF9, 6YFA, 6YFB, 6YFC, 6YFD, 6YFE, 6YFF, 6YFG, 6YFH, 6YFI, 6YFJ, 6YFK, 6YFL, 6YFM, 6YFN, 6YFO, 6YFP, 6YFQ, 6YFR, 6YFS, 6YFT, 6YFU

  • PubMed Abstract: 
  • The single-stranded RNA (ssRNA) bacteriophages are among the simplest known viruses with small genomes and exceptionally high mutation rates. The number of ssRNA phage isolates has remained very low, but recent metagenomic studies have uncovered an immense variety of distinct uncultured ssRNA phages ...

    The single-stranded RNA (ssRNA) bacteriophages are among the simplest known viruses with small genomes and exceptionally high mutation rates. The number of ssRNA phage isolates has remained very low, but recent metagenomic studies have uncovered an immense variety of distinct uncultured ssRNA phages. The coat proteins (CPs) in these genomes are particularly diverse, with notable variation in length and often no recognizable similarity to previously known viruses. We recombinantly expressed metagenome-derived ssRNA phage CPs to produce virus-like particles and determined the three-dimensional structure of 22 previously uncharacterized ssRNA phage capsids covering nine distinct CP types. The structures revealed substantial deviations from the previously known ssRNA phage CP fold, uncovered an unusual prolate particle shape, and revealed a previously unseen dsRNA binding mode. These data expand our knowledge of the evolution of viral structural proteins and are of relevance for applications such as ssRNA phage-based vaccine design.


    Organizational Affiliation

    Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia. kaspars@biomed.lu.lv.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
coat protein
A [auth AA],
B [auth AB],
C [auth AC],
D [auth AD],
E [auth AE],
F [auth AF],
G [auth AG],
H [auth AH],
I [auth AI],
J [auth AJ],
K [auth AK],
L [auth AL],
M [auth AM],
N [auth AN],
O [auth AO],
P [auth AP],
Q [auth AQ],
R [auth AR],
S [auth AS],
T [auth AT],
U [auth AU],
V [auth AV],
W [auth AW],
X [auth AX],
Y [auth AY],
Z [auth AZ],
AA [auth BA],
BA [auth BB],
CA [auth BC],
DA [auth BD],
EA [auth BE],
FA [auth BF],
GA [auth BG],
HA [auth BH],
IA [auth BI],
JA [auth BJ],
KA [auth BK],
LA [auth BL],
MA [auth BM],
NA [auth BN],
OA [auth BO],
PA [auth BP],
QA [auth BQ],
RA [auth BR],
SA [auth BS],
TA [auth BT],
UA [auth BU],
VA [auth BV],
WA [auth BW],
XA [auth BX],
YA [auth BY],
ZA [auth BZ],
AB [auth CA],
BB [auth CB],
CB [auth CC],
DB [auth CD],
EB [auth CE],
FB [auth CF],
GB [auth CG],
HB [auth CH],
IB [auth CI],
JB [auth CJ],
KB [auth CK],
LB [auth CL],
MB [auth CM],
NB [auth CN],
OB [auth CO],
PB [auth CP],
QB [auth CQ],
RB [auth CR],
SB [auth CS],
TB [auth CT],
UB [auth CU],
VB [auth CV],
WB [auth CW],
XB [auth CX],
YB [auth CY],
ZB [auth CZ],
AC [auth DA],
BC [auth DB],
CC [auth DC],
DC [auth DD],
EC [auth DE],
FC [auth DF],
GC [auth DG],
HC [auth DH],
IC [auth DI],
JC [auth DJ],
KC [auth DK],
LC [auth DL],
MC [auth DM],
NC [auth DN],
OC [auth DO],
PC [auth DP],
QC [auth DQ],
RC [auth DR],
SC [auth DS],
TC [auth DT],
UC [auth DU],
VC [auth DV],
WC [auth DW],
XC [auth DX],
YC [auth DY],
ZC [auth DZ],
AD [auth EA],
BD [auth EB],
CD [auth EC],
DD [auth ED],
ED [auth EE],
FD [auth EF],
GD [auth EG],
HD [auth EH],
ID [auth EI],
JD [auth EJ],
KD [auth EK],
LD [auth EL],
MD [auth EM],
ND [auth EN],
OD [auth EO],
PD [auth EP],
QD [auth EQ],
RD [auth ER],
SD [auth ES],
TD [auth ET],
UD [auth EU],
VD [auth EV],
WD [auth EW],
XD [auth EX],
YD [auth EY],
ZD [auth EZ],
AE [auth FA],
BE [auth FB],
CE [auth FC],
DE [auth FD],
EE [auth FE],
FE [auth FF],
GE [auth FG],
HE [auth FH],
IE [auth FI],
JE [auth FJ],
KE [auth FK],
LE [auth FL],
ME [auth FM],
NE [auth FN],
OE [auth FO],
PE [auth FP],
QE [auth FQ],
RE [auth FR],
SE [auth FS],
TE [auth FT],
UE [auth FU],
VE [auth FV],
WE [auth FW],
XE [auth FX],
YE [auth FY],
ZE [auth FZ],
AF [auth GA],
BF [auth GB],
CF [auth GC],
DF [auth GD],
EF [auth GE],
FF [auth GF],
GF [auth GG],
HF [auth GH],
IF [auth GI],
JF [auth GJ],
KF [auth GK],
LF [auth GL],
MF [auth GM],
NF [auth GN],
OF [auth GO],
PF [auth GP],
QF [auth GQ],
RF [auth GR],
SF [auth GS],
TF [auth GT],
UF [auth GU],
VF [auth GV],
WF [auth GW],
XF [auth GX],
YF [auth GY],
ZF [auth GZ],
AG [auth HA],
BG [auth HB],
CG [auth HC],
DG [auth HD],
EG [auth HE],
FG [auth HF],
GG [auth HG],
HG [auth HH],
IG [auth HI],
JG [auth HJ],
KG [auth HK],
LG [auth HL],
MG [auth HM],
NG [auth HN],
OG [auth HO],
PG [auth HP],
QG [auth HQ],
RG [auth HR],
SG [auth HS],
TG [auth HT],
UG [auth HU],
VG [auth HV],
WG [auth HW],
XG [auth HX],
YG [auth HY],
ZG [auth HZ],
AH [auth IA],
BH [auth IB]
166Leviviridae sp.Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 325.466α = 90
b = 298.52β = 100
c = 417.119γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
FFTphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Regional Development FundLatvia1.1.1.1/16/A/104

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references