7A4F

Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-1 (120-mer)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein.

Tetter, S.Terasaka, N.Steinauer, A.Bingham, R.J.Clark, S.Scott, A.J.P.Patel, N.Leibundgut, M.Wroblewski, E.Ban, N.Stockley, P.G.Twarock, R.Hilvert, D.

(2021) Science 372: 1220-1224

  • DOI: https://doi.org/10.1126/science.abg2822
  • Primary Citation of Related Structures:  
    7A4F, 7A4G, 7A4H, 7A4I, 7A4J

  • PubMed Abstract: 

    Viruses are ubiquitous pathogens of global impact. Prompted by the hypothesis that their earliest progenitors recruited host proteins for virion formation, we have used stringent laboratory evolution to convert a bacterial enzyme that lacks affinity for nucleic acids into an artificial nucleocapsid that efficiently packages and protects multiple copies of its own encoding messenger RNA. Revealing remarkable convergence on the molecular hallmarks of natural viruses, the accompanying changes reorganized the protein building blocks into an interlaced 240-subunit icosahedral capsid that is impermeable to nucleases, and emergence of a robust RNA stem-loop packaging cassette ensured high encapsidation yields and specificity. In addition to evincing a plausible evolutionary pathway for primordial viruses, these findings highlight practical strategies for developing nonviral carriers for diverse vaccine and delivery applications.


  • Organizational Affiliation

    Departments of Mathematics and Biology, University of York, York YO10 5DD, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
A [auth AA],
AA [auth CG],
AB [auth FC],
AC [auth HI],
AD [auth KE],
B [auth AB],
BA [auth CH],
BB [auth FD],
BC [auth HJ],
BD [auth KF],
C [auth AC],
CA [auth CI],
CB [auth FE],
CC [auth IA],
CD [auth KG],
D [auth AD],
DA [auth CJ],
DB [auth FF],
DC [auth IB],
DD [auth KH],
E [auth AE],
EA [auth DA],
EB [auth FG],
EC [auth IC],
ED [auth KI],
F [auth AF],
FA [auth DB],
FB [auth FH],
FC [auth ID],
FD [auth KJ],
G [auth AG],
GA [auth DC],
GB [auth FI],
GC [auth IE],
GD [auth LA],
H [auth AH],
HA [auth DD],
HB [auth FJ],
HC [auth IF],
HD [auth LB],
I [auth AI],
IA [auth DE],
IB [auth GA],
IC [auth IG],
ID [auth LC],
J [auth AJ],
JA [auth DF],
JB [auth GB],
JC [auth IH],
JD [auth LD],
K [auth BA],
KA [auth DG],
KB [auth GC],
KC [auth II],
KD [auth LE],
L [auth BB],
LA [auth DH],
LB [auth GD],
LC [auth IJ],
LD [auth LF],
M [auth BC],
MA [auth DI],
MB [auth GE],
MC [auth JA],
MD [auth LG],
N [auth BD],
NA [auth DJ],
NB [auth GF],
NC [auth JB],
ND [auth LH],
O [auth BE],
OA [auth EA],
OB [auth GG],
OC [auth JC],
OD [auth LI],
P [auth BF],
PA [auth EB],
PB [auth GH],
PC [auth JD],
PD [auth LJ],
Q [auth BG],
QA [auth EC],
QB [auth GI],
QC [auth JE],
R [auth BH],
RA [auth ED],
RB [auth GJ],
RC [auth JF],
S [auth BI],
SA [auth EE],
SB [auth HA],
SC [auth JG],
T [auth BJ],
TA [auth EF],
TB [auth HB],
TC [auth JH],
U [auth CA],
UA [auth EG],
UB [auth HC],
UC [auth JI],
V [auth CB],
VA [auth EH],
VB [auth HD],
VC [auth JJ],
W [auth CC],
WA [auth EI],
WB [auth HE],
WC [auth KA],
X [auth CD],
XA [auth EJ],
XB [auth HF],
XC [auth KB],
Y [auth CE],
YA [auth FA],
YB [auth HG],
YC [auth KC],
Z [auth CF],
ZA [auth FB],
ZB [auth HH],
ZC [auth KD]
197Lambdavirus lambdaAquifex aeolicus VF5Mutation(s): 1 
Gene Names: Nlambdap49ribHaq_132
EC: 2.5.1.78
UniProt
Find proteins for O66529 (Aquifex aeolicus (strain VF5))
Explore O66529 
Go to UniProtKB:  O66529
Find proteins for P03045 (Escherichia phage lambda)
Explore P03045 
Go to UniProtKB:  P03045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP03045O66529
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.18

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)ERC-AdG-2012-321295

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 1.2: 2021-06-23
    Changes: Database references