Virus-like particle of bacteriophage AVE016

Experimental Data Snapshot

  • 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 1.2 of the entry. See complete history


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: https://doi.org/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 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.

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

Experimental Data

  • 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
PDB_EXTRACTdata extraction

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
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description