7A4J

Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 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 GC],
AB [auth MA],
AC [auth QC],
AD [auth XA],
AE [auth dC],
AF [auth kA],
AG [auth qC],
AH [auth xA],
AI [auth 3C],
B [auth AB],
BA [auth GD],
BB [auth MB],
BC [auth QD],
BD [auth XB],
BE [auth dD],
BF [auth kB],
BG [auth qD],
BH [auth xB],
BI [auth 3D],
C [auth AC],
CA [auth HA],
CB [auth MC],
CC [auth RA],
CD [auth XC],
CE [auth eA],
CF [auth kC],
CG [auth rA],
CH [auth xC],
CI [auth 4A],
D [auth AD],
DA [auth HB],
DB [auth MD],
DC [auth RB],
DD [auth XD],
DE [auth eB],
DF [auth kD],
DG [auth rB],
DH [auth xD],
DI [auth 4B],
E [auth BA],
EA [auth HC],
EB [auth NA],
EC [auth RC],
ED [auth YA],
EE [auth eC],
EF [auth lA],
EG [auth rC],
EH [auth yA],
EI [auth 4C],
F [auth BB],
FA [auth HD],
FB [auth NB],
FC [auth RD],
FD [auth YB],
FE [auth eD],
FF [auth lB],
FG [auth rD],
FH [auth yB],
FI [auth 4D],
G [auth BC],
GA [auth IA],
GB [auth NC],
GC [auth SA],
GD [auth YC],
GE [auth fA],
GF [auth lC],
GG [auth sA],
GH [auth yC],
H [auth BD],
HA [auth IB],
HB [auth ND],
HC [auth SB],
HD [auth YD],
HE [auth fB],
HF [auth lD],
HG [auth sB],
HH [auth yD],
I [auth CA],
IA [auth IC],
IB [auth OA],
IC [auth SC],
ID [auth ZA],
IE [auth fC],
IF [auth mA],
IG [auth sC],
IH [auth zA],
J [auth CB],
JA [auth ID],
JB [auth OB],
JC [auth SD],
JD [auth ZB],
JE [auth fD],
JF [auth mB],
JG [auth sD],
JH [auth zB],
K [auth CC],
KA [auth 5A],
KB [auth OC],
KC [auth TA],
KD [auth ZC],
KE [auth gA],
KF [auth mC],
KG [auth tA],
KH [auth zC],
L [auth CD],
LA [auth 5B],
LB [auth OD],
LC [auth TB],
LD [auth ZD],
LE [auth gB],
LF [auth mD],
LG [auth tB],
LH [auth zD],
M [auth DA],
MA [auth 5C],
MB [auth PA],
MC [auth TC],
MD [auth aA],
ME [auth gC],
MF [auth nA],
MG [auth tC],
MH [auth 0A],
N [auth DB],
NA [auth 5D],
NB [auth PB],
NC [auth TD],
ND [auth aB],
NE [auth gD],
NF [auth nB],
NG [auth tD],
NH [auth 0B],
O [auth DC],
OA [auth JA],
OB [auth PC],
OC [auth UA],
OD [auth aC],
OE [auth hA],
OF [auth nC],
OG [auth uA],
OH [auth 0C],
P [auth DD],
PA [auth JB],
PB [auth PD],
PC [auth UB],
PD [auth aD],
PE [auth hB],
PF [auth nD],
PG [auth uB],
PH [auth 0D],
Q [auth EA],
QA [auth JC],
QB [auth 6A],
QC [auth UC],
QD [auth bA],
QE [auth hC],
QF [auth oA],
QG [auth uC],
QH [auth 1A],
R [auth EB],
RA [auth JD],
RB [auth 6B],
RC [auth UD],
RD [auth bB],
RE [auth hD],
RF [auth oB],
RG [auth uD],
RH [auth 1B],
S [auth EC],
SA [auth KA],
SB [auth 6C],
SC [auth VA],
SD [auth bC],
SE [auth iA],
SF [auth oC],
SG [auth vA],
SH [auth 1C],
T [auth ED],
TA [auth KB],
TB [auth 6D],
TC [auth VB],
TD [auth bD],
TE [auth iB],
TF [auth oD],
TG [auth vB],
TH [auth 1D],
U [auth FA],
UA [auth KC],
UB [auth 7A],
UC [auth VC],
UD [auth cA],
UE [auth iC],
UF [auth pA],
UG [auth vC],
UH [auth 2A],
V [auth FB],
VA [auth KD],
VB [auth 7B],
VC [auth VD],
VD [auth cB],
VE [auth iD],
VF [auth pB],
VG [auth vD],
VH [auth 2B],
W [auth FC],
WA [auth LA],
WB [auth 7C],
WC [auth WA],
WD [auth cC],
WE [auth jA],
WF [auth pC],
WG [auth wA],
WH [auth 2C],
X [auth FD],
XA [auth LB],
XB [auth 7D],
XC [auth WB],
XD [auth cD],
XE [auth jB],
XF [auth pD],
XG [auth wB],
XH [auth 2D],
Y [auth GA],
YA [auth LC],
YB [auth QA],
YC [auth WC],
YD [auth dA],
YE [auth jC],
YF [auth qA],
YG [auth wC],
YH [auth 3A],
Z [auth GB],
ZA [auth LD],
ZB [auth QB],
ZC [auth WD],
ZD [auth dB],
ZE [auth jD],
ZF [auth qB],
ZG [auth wD],
ZH [auth 3B]
197Lambdavirus lambdaAquifex aeolicus VF5Mutation(s): 15 
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: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
RECONSTRUCTIONRELION3.0

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