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- PDB-28ro: split variant of Aquifex aeolicus lumazine synthase-derived nucle... -

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Basic information

Entry
Database: PDB / ID: 28ro
Titlesplit variant of Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-4
Components(6,7-dimethyl-8-ribityllumazine synthase) x 2
KeywordsVIRUS LIKE PARTICLE / capsid / design / virus mimic
Function / homology
Function and homology information


6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / cytoplasm / cytosol
Similarity search - Function
Lumazine synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Domain/homology
6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsTetter, S. / Hilvert, D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-AdG-2012-321295European Union
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2026
Title: An engineered closed-shell, two-component, 480-subunit nucleocapsid.
Authors: Mikail D Levasseur / Naohiro Terasaka / Angela Steinauer / Stephan Tetter / Sara Pfister / Beat H Meier / Donald Hilvert /
Abstract: Self-assembling protein cages are valuable nanoscale containers for biotechnology and medical applications. Two-component systems are especially attractive due to their potential for functional ...Self-assembling protein cages are valuable nanoscale containers for biotechnology and medical applications. Two-component systems are especially attractive due to their potential for functional complexity. In this study, we demonstrate that the subunits of the 240-subunit nucleocapsid NC-4, which was previously evolved to package and protect its encoding mRNA, can be split into two fragments without disrupting cage assembly or structure, generating a two-component, 480-subunit capsid. This modification introduces additional termini on the cage's exterior surface, creating opportunities for functionalization. We exploited these new sites by genetically appending peptide and protein tags to the exterior surface of split NC-4 (spNC-4), enabling site-specific glycosylation via posttranslational modification and cell-specific delivery by targeted antibody recruitment. Our findings broaden the utility of the NC-4 nucleocapsid. By extension, splitting related protein compartments that bind diverse cargoes could offer a robust platform for biotechnological applications requiring simultaneous encapsulation and customizable surface modification.
#1: Journal: Biorxiv / Year: 2025
Title: An engineered closed-shell, two-component, 480-subunit nucleocapsid
Authors: Levasseur, M.D. / Terasaka, N. / Steinauer, A. / Tetter, S. / Pfister, S. / Meier, B.H. / Hilvert, D.
History
DepositionFeb 16, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 1.1Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0A: 6,7-dimethyl-8-ribityllumazine synthase
0B: 6,7-dimethyl-8-ribityllumazine synthase
0C: 6,7-dimethyl-8-ribityllumazine synthase
0D: 6,7-dimethyl-8-ribityllumazine synthase
0a: 6,7-dimethyl-8-ribityllumazine synthase
0b: 6,7-dimethyl-8-ribityllumazine synthase
0c: 6,7-dimethyl-8-ribityllumazine synthase
0d: 6,7-dimethyl-8-ribityllumazine synthase
1A: 6,7-dimethyl-8-ribityllumazine synthase
1B: 6,7-dimethyl-8-ribityllumazine synthase
1C: 6,7-dimethyl-8-ribityllumazine synthase
1D: 6,7-dimethyl-8-ribityllumazine synthase
1a: 6,7-dimethyl-8-ribityllumazine synthase
1b: 6,7-dimethyl-8-ribityllumazine synthase
1c: 6,7-dimethyl-8-ribityllumazine synthase
1d: 6,7-dimethyl-8-ribityllumazine synthase
2A: 6,7-dimethyl-8-ribityllumazine synthase
2B: 6,7-dimethyl-8-ribityllumazine synthase
2C: 6,7-dimethyl-8-ribityllumazine synthase
2D: 6,7-dimethyl-8-ribityllumazine synthase
2a: 6,7-dimethyl-8-ribityllumazine synthase
2b: 6,7-dimethyl-8-ribityllumazine synthase
2c: 6,7-dimethyl-8-ribityllumazine synthase
2d: 6,7-dimethyl-8-ribityllumazine synthase
3A: 6,7-dimethyl-8-ribityllumazine synthase
3B: 6,7-dimethyl-8-ribityllumazine synthase
3C: 6,7-dimethyl-8-ribityllumazine synthase
3D: 6,7-dimethyl-8-ribityllumazine synthase
3a: 6,7-dimethyl-8-ribityllumazine synthase
3b: 6,7-dimethyl-8-ribityllumazine synthase
3c: 6,7-dimethyl-8-ribityllumazine synthase
3d: 6,7-dimethyl-8-ribityllumazine synthase
4A: 6,7-dimethyl-8-ribityllumazine synthase
4B: 6,7-dimethyl-8-ribityllumazine synthase
4C: 6,7-dimethyl-8-ribityllumazine synthase
4D: 6,7-dimethyl-8-ribityllumazine synthase
4a: 6,7-dimethyl-8-ribityllumazine synthase
4b: 6,7-dimethyl-8-ribityllumazine synthase
4c: 6,7-dimethyl-8-ribityllumazine synthase
4d: 6,7-dimethyl-8-ribityllumazine synthase
5A: 6,7-dimethyl-8-ribityllumazine synthase
5B: 6,7-dimethyl-8-ribityllumazine synthase
5C: 6,7-dimethyl-8-ribityllumazine synthase
5D: 6,7-dimethyl-8-ribityllumazine synthase
5a: 6,7-dimethyl-8-ribityllumazine synthase
5b: 6,7-dimethyl-8-ribityllumazine synthase
5c: 6,7-dimethyl-8-ribityllumazine synthase
5d: 6,7-dimethyl-8-ribityllumazine synthase
6A: 6,7-dimethyl-8-ribityllumazine synthase
6B: 6,7-dimethyl-8-ribityllumazine synthase
6C: 6,7-dimethyl-8-ribityllumazine synthase
6D: 6,7-dimethyl-8-ribityllumazine synthase
6a: 6,7-dimethyl-8-ribityllumazine synthase
6b: 6,7-dimethyl-8-ribityllumazine synthase
6c: 6,7-dimethyl-8-ribityllumazine synthase
6d: 6,7-dimethyl-8-ribityllumazine synthase
7A: 6,7-dimethyl-8-ribityllumazine synthase
7B: 6,7-dimethyl-8-ribityllumazine synthase
7C: 6,7-dimethyl-8-ribityllumazine synthase
7D: 6,7-dimethyl-8-ribityllumazine synthase
7a: 6,7-dimethyl-8-ribityllumazine synthase
7b: 6,7-dimethyl-8-ribityllumazine synthase
7c: 6,7-dimethyl-8-ribityllumazine synthase
7d: 6,7-dimethyl-8-ribityllumazine synthase
AA: 6,7-dimethyl-8-ribityllumazine synthase
AB: 6,7-dimethyl-8-ribityllumazine synthase
AC: 6,7-dimethyl-8-ribityllumazine synthase
AD: 6,7-dimethyl-8-ribityllumazine synthase
Aa: 6,7-dimethyl-8-ribityllumazine synthase
Ab: 6,7-dimethyl-8-ribityllumazine synthase
Ac: 6,7-dimethyl-8-ribityllumazine synthase
Ad: 6,7-dimethyl-8-ribityllumazine synthase
BA: 6,7-dimethyl-8-ribityllumazine synthase
BB: 6,7-dimethyl-8-ribityllumazine synthase
BC: 6,7-dimethyl-8-ribityllumazine synthase
BD: 6,7-dimethyl-8-ribityllumazine synthase
Ba: 6,7-dimethyl-8-ribityllumazine synthase
Bb: 6,7-dimethyl-8-ribityllumazine synthase
Bc: 6,7-dimethyl-8-ribityllumazine synthase
Bd: 6,7-dimethyl-8-ribityllumazine synthase
CA: 6,7-dimethyl-8-ribityllumazine synthase
CB: 6,7-dimethyl-8-ribityllumazine synthase
CC: 6,7-dimethyl-8-ribityllumazine synthase
CD: 6,7-dimethyl-8-ribityllumazine synthase
Ca: 6,7-dimethyl-8-ribityllumazine synthase
Cb: 6,7-dimethyl-8-ribityllumazine synthase
Cc: 6,7-dimethyl-8-ribityllumazine synthase
Cd: 6,7-dimethyl-8-ribityllumazine synthase
DA: 6,7-dimethyl-8-ribityllumazine synthase
DB: 6,7-dimethyl-8-ribityllumazine synthase
DC: 6,7-dimethyl-8-ribityllumazine synthase
DD: 6,7-dimethyl-8-ribityllumazine synthase
Da: 6,7-dimethyl-8-ribityllumazine synthase
Db: 6,7-dimethyl-8-ribityllumazine synthase
Dc: 6,7-dimethyl-8-ribityllumazine synthase
Dd: 6,7-dimethyl-8-ribityllumazine synthase
EA: 6,7-dimethyl-8-ribityllumazine synthase
EB: 6,7-dimethyl-8-ribityllumazine synthase
EC: 6,7-dimethyl-8-ribityllumazine synthase
ED: 6,7-dimethyl-8-ribityllumazine synthase
Ea: 6,7-dimethyl-8-ribityllumazine synthase
Eb: 6,7-dimethyl-8-ribityllumazine synthase
Ec: 6,7-dimethyl-8-ribityllumazine synthase
Ed: 6,7-dimethyl-8-ribityllumazine synthase
FA: 6,7-dimethyl-8-ribityllumazine synthase
FB: 6,7-dimethyl-8-ribityllumazine synthase
FC: 6,7-dimethyl-8-ribityllumazine synthase
FD: 6,7-dimethyl-8-ribityllumazine synthase
Fa: 6,7-dimethyl-8-ribityllumazine synthase
Fb: 6,7-dimethyl-8-ribityllumazine synthase
Fc: 6,7-dimethyl-8-ribityllumazine synthase
Fd: 6,7-dimethyl-8-ribityllumazine synthase
GA: 6,7-dimethyl-8-ribityllumazine synthase
GB: 6,7-dimethyl-8-ribityllumazine synthase
GC: 6,7-dimethyl-8-ribityllumazine synthase
GD: 6,7-dimethyl-8-ribityllumazine synthase
Ga: 6,7-dimethyl-8-ribityllumazine synthase
Gb: 6,7-dimethyl-8-ribityllumazine synthase
Gc: 6,7-dimethyl-8-ribityllumazine synthase
Gd: 6,7-dimethyl-8-ribityllumazine synthase
HA: 6,7-dimethyl-8-ribityllumazine synthase
HB: 6,7-dimethyl-8-ribityllumazine synthase
HC: 6,7-dimethyl-8-ribityllumazine synthase
HD: 6,7-dimethyl-8-ribityllumazine synthase
Ha: 6,7-dimethyl-8-ribityllumazine synthase
Hb: 6,7-dimethyl-8-ribityllumazine synthase
Hc: 6,7-dimethyl-8-ribityllumazine synthase
Hd: 6,7-dimethyl-8-ribityllumazine synthase
IA: 6,7-dimethyl-8-ribityllumazine synthase
IB: 6,7-dimethyl-8-ribityllumazine synthase
IC: 6,7-dimethyl-8-ribityllumazine synthase
ID: 6,7-dimethyl-8-ribityllumazine synthase
Ia: 6,7-dimethyl-8-ribityllumazine synthase
Ib: 6,7-dimethyl-8-ribityllumazine synthase
Ic: 6,7-dimethyl-8-ribityllumazine synthase
Id: 6,7-dimethyl-8-ribityllumazine synthase
JA: 6,7-dimethyl-8-ribityllumazine synthase
JB: 6,7-dimethyl-8-ribityllumazine synthase
JC: 6,7-dimethyl-8-ribityllumazine synthase
JD: 6,7-dimethyl-8-ribityllumazine synthase
Ja: 6,7-dimethyl-8-ribityllumazine synthase
Jb: 6,7-dimethyl-8-ribityllumazine synthase
Jc: 6,7-dimethyl-8-ribityllumazine synthase
Jd: 6,7-dimethyl-8-ribityllumazine synthase
KA: 6,7-dimethyl-8-ribityllumazine synthase
KB: 6,7-dimethyl-8-ribityllumazine synthase
KC: 6,7-dimethyl-8-ribityllumazine synthase
KD: 6,7-dimethyl-8-ribityllumazine synthase
Ka: 6,7-dimethyl-8-ribityllumazine synthase
Kb: 6,7-dimethyl-8-ribityllumazine synthase
Kc: 6,7-dimethyl-8-ribityllumazine synthase
Kd: 6,7-dimethyl-8-ribityllumazine synthase
LA: 6,7-dimethyl-8-ribityllumazine synthase
LB: 6,7-dimethyl-8-ribityllumazine synthase
LC: 6,7-dimethyl-8-ribityllumazine synthase
LD: 6,7-dimethyl-8-ribityllumazine synthase
La: 6,7-dimethyl-8-ribityllumazine synthase
Lb: 6,7-dimethyl-8-ribityllumazine synthase
Lc: 6,7-dimethyl-8-ribityllumazine synthase
Ld: 6,7-dimethyl-8-ribityllumazine synthase
MA: 6,7-dimethyl-8-ribityllumazine synthase
MB: 6,7-dimethyl-8-ribityllumazine synthase
MC: 6,7-dimethyl-8-ribityllumazine synthase
MD: 6,7-dimethyl-8-ribityllumazine synthase
Ma: 6,7-dimethyl-8-ribityllumazine synthase
Mb: 6,7-dimethyl-8-ribityllumazine synthase
Mc: 6,7-dimethyl-8-ribityllumazine synthase
Md: 6,7-dimethyl-8-ribityllumazine synthase
NA: 6,7-dimethyl-8-ribityllumazine synthase
NB: 6,7-dimethyl-8-ribityllumazine synthase
NC: 6,7-dimethyl-8-ribityllumazine synthase
ND: 6,7-dimethyl-8-ribityllumazine synthase
Na: 6,7-dimethyl-8-ribityllumazine synthase
Nb: 6,7-dimethyl-8-ribityllumazine synthase
Nc: 6,7-dimethyl-8-ribityllumazine synthase
Nd: 6,7-dimethyl-8-ribityllumazine synthase
OA: 6,7-dimethyl-8-ribityllumazine synthase
OB: 6,7-dimethyl-8-ribityllumazine synthase
OC: 6,7-dimethyl-8-ribityllumazine synthase
OD: 6,7-dimethyl-8-ribityllumazine synthase
Oa: 6,7-dimethyl-8-ribityllumazine synthase
Ob: 6,7-dimethyl-8-ribityllumazine synthase
Oc: 6,7-dimethyl-8-ribityllumazine synthase
Od: 6,7-dimethyl-8-ribityllumazine synthase
PA: 6,7-dimethyl-8-ribityllumazine synthase
PB: 6,7-dimethyl-8-ribityllumazine synthase
PC: 6,7-dimethyl-8-ribityllumazine synthase
PD: 6,7-dimethyl-8-ribityllumazine synthase
Pa: 6,7-dimethyl-8-ribityllumazine synthase
Pb: 6,7-dimethyl-8-ribityllumazine synthase
Pc: 6,7-dimethyl-8-ribityllumazine synthase
Pd: 6,7-dimethyl-8-ribityllumazine synthase
QA: 6,7-dimethyl-8-ribityllumazine synthase
QB: 6,7-dimethyl-8-ribityllumazine synthase
QC: 6,7-dimethyl-8-ribityllumazine synthase
QD: 6,7-dimethyl-8-ribityllumazine synthase
Qa: 6,7-dimethyl-8-ribityllumazine synthase
Qb: 6,7-dimethyl-8-ribityllumazine synthase
Qc: 6,7-dimethyl-8-ribityllumazine synthase
Qd: 6,7-dimethyl-8-ribityllumazine synthase
RA: 6,7-dimethyl-8-ribityllumazine synthase
RB: 6,7-dimethyl-8-ribityllumazine synthase
RC: 6,7-dimethyl-8-ribityllumazine synthase
RD: 6,7-dimethyl-8-ribityllumazine synthase
Ra: 6,7-dimethyl-8-ribityllumazine synthase
Rb: 6,7-dimethyl-8-ribityllumazine synthase
Rc: 6,7-dimethyl-8-ribityllumazine synthase
Rd: 6,7-dimethyl-8-ribityllumazine synthase
SA: 6,7-dimethyl-8-ribityllumazine synthase
SB: 6,7-dimethyl-8-ribityllumazine synthase
SC: 6,7-dimethyl-8-ribityllumazine synthase
SD: 6,7-dimethyl-8-ribityllumazine synthase
Sa: 6,7-dimethyl-8-ribityllumazine synthase
Sb: 6,7-dimethyl-8-ribityllumazine synthase
Sc: 6,7-dimethyl-8-ribityllumazine synthase
Sd: 6,7-dimethyl-8-ribityllumazine synthase
TA: 6,7-dimethyl-8-ribityllumazine synthase
TB: 6,7-dimethyl-8-ribityllumazine synthase
TC: 6,7-dimethyl-8-ribityllumazine synthase
TD: 6,7-dimethyl-8-ribityllumazine synthase
Ta: 6,7-dimethyl-8-ribityllumazine synthase
Tb: 6,7-dimethyl-8-ribityllumazine synthase
Tc: 6,7-dimethyl-8-ribityllumazine synthase
Td: 6,7-dimethyl-8-ribityllumazine synthase
UA: 6,7-dimethyl-8-ribityllumazine synthase
UB: 6,7-dimethyl-8-ribityllumazine synthase
UC: 6,7-dimethyl-8-ribityllumazine synthase
UD: 6,7-dimethyl-8-ribityllumazine synthase
Ua: 6,7-dimethyl-8-ribityllumazine synthase
Ub: 6,7-dimethyl-8-ribityllumazine synthase
Uc: 6,7-dimethyl-8-ribityllumazine synthase
Ud: 6,7-dimethyl-8-ribityllumazine synthase
VA: 6,7-dimethyl-8-ribityllumazine synthase
VB: 6,7-dimethyl-8-ribityllumazine synthase
VC: 6,7-dimethyl-8-ribityllumazine synthase
VD: 6,7-dimethyl-8-ribityllumazine synthase
Va: 6,7-dimethyl-8-ribityllumazine synthase
Vb: 6,7-dimethyl-8-ribityllumazine synthase
Vc: 6,7-dimethyl-8-ribityllumazine synthase
Vd: 6,7-dimethyl-8-ribityllumazine synthase
WA: 6,7-dimethyl-8-ribityllumazine synthase
WB: 6,7-dimethyl-8-ribityllumazine synthase
WC: 6,7-dimethyl-8-ribityllumazine synthase
WD: 6,7-dimethyl-8-ribityllumazine synthase
Wa: 6,7-dimethyl-8-ribityllumazine synthase
Wb: 6,7-dimethyl-8-ribityllumazine synthase
Wc: 6,7-dimethyl-8-ribityllumazine synthase
Wd: 6,7-dimethyl-8-ribityllumazine synthase
XA: 6,7-dimethyl-8-ribityllumazine synthase
XB: 6,7-dimethyl-8-ribityllumazine synthase
XC: 6,7-dimethyl-8-ribityllumazine synthase
XD: 6,7-dimethyl-8-ribityllumazine synthase
Xa: 6,7-dimethyl-8-ribityllumazine synthase
Xb: 6,7-dimethyl-8-ribityllumazine synthase
Xc: 6,7-dimethyl-8-ribityllumazine synthase
Xd: 6,7-dimethyl-8-ribityllumazine synthase
YA: 6,7-dimethyl-8-ribityllumazine synthase
YB: 6,7-dimethyl-8-ribityllumazine synthase
YC: 6,7-dimethyl-8-ribityllumazine synthase
YD: 6,7-dimethyl-8-ribityllumazine synthase
Ya: 6,7-dimethyl-8-ribityllumazine synthase
Yb: 6,7-dimethyl-8-ribityllumazine synthase
Yc: 6,7-dimethyl-8-ribityllumazine synthase
Yd: 6,7-dimethyl-8-ribityllumazine synthase
ZA: 6,7-dimethyl-8-ribityllumazine synthase
ZB: 6,7-dimethyl-8-ribityllumazine synthase
ZC: 6,7-dimethyl-8-ribityllumazine synthase
ZD: 6,7-dimethyl-8-ribityllumazine synthase
Za: 6,7-dimethyl-8-ribityllumazine synthase
Zb: 6,7-dimethyl-8-ribityllumazine synthase
Zc: 6,7-dimethyl-8-ribityllumazine synthase
Zd: 6,7-dimethyl-8-ribityllumazine synthase
aA: 6,7-dimethyl-8-ribityllumazine synthase
aB: 6,7-dimethyl-8-ribityllumazine synthase
aC: 6,7-dimethyl-8-ribityllumazine synthase
aD: 6,7-dimethyl-8-ribityllumazine synthase
aa: 6,7-dimethyl-8-ribityllumazine synthase
ab: 6,7-dimethyl-8-ribityllumazine synthase
ac: 6,7-dimethyl-8-ribityllumazine synthase
ad: 6,7-dimethyl-8-ribityllumazine synthase
bA: 6,7-dimethyl-8-ribityllumazine synthase
bB: 6,7-dimethyl-8-ribityllumazine synthase
bC: 6,7-dimethyl-8-ribityllumazine synthase
bD: 6,7-dimethyl-8-ribityllumazine synthase
ba: 6,7-dimethyl-8-ribityllumazine synthase
bb: 6,7-dimethyl-8-ribityllumazine synthase
bc: 6,7-dimethyl-8-ribityllumazine synthase
bd: 6,7-dimethyl-8-ribityllumazine synthase
cA: 6,7-dimethyl-8-ribityllumazine synthase
cB: 6,7-dimethyl-8-ribityllumazine synthase
cC: 6,7-dimethyl-8-ribityllumazine synthase
cD: 6,7-dimethyl-8-ribityllumazine synthase
ca: 6,7-dimethyl-8-ribityllumazine synthase
cb: 6,7-dimethyl-8-ribityllumazine synthase
cc: 6,7-dimethyl-8-ribityllumazine synthase
cd: 6,7-dimethyl-8-ribityllumazine synthase
dA: 6,7-dimethyl-8-ribityllumazine synthase
dB: 6,7-dimethyl-8-ribityllumazine synthase
dC: 6,7-dimethyl-8-ribityllumazine synthase
dD: 6,7-dimethyl-8-ribityllumazine synthase
da: 6,7-dimethyl-8-ribityllumazine synthase
db: 6,7-dimethyl-8-ribityllumazine synthase
dc: 6,7-dimethyl-8-ribityllumazine synthase
dd: 6,7-dimethyl-8-ribityllumazine synthase
eA: 6,7-dimethyl-8-ribityllumazine synthase
eB: 6,7-dimethyl-8-ribityllumazine synthase
eC: 6,7-dimethyl-8-ribityllumazine synthase
eD: 6,7-dimethyl-8-ribityllumazine synthase
ea: 6,7-dimethyl-8-ribityllumazine synthase
eb: 6,7-dimethyl-8-ribityllumazine synthase
ec: 6,7-dimethyl-8-ribityllumazine synthase
ed: 6,7-dimethyl-8-ribityllumazine synthase
fA: 6,7-dimethyl-8-ribityllumazine synthase
fB: 6,7-dimethyl-8-ribityllumazine synthase
fC: 6,7-dimethyl-8-ribityllumazine synthase
fD: 6,7-dimethyl-8-ribityllumazine synthase
fa: 6,7-dimethyl-8-ribityllumazine synthase
fb: 6,7-dimethyl-8-ribityllumazine synthase
fc: 6,7-dimethyl-8-ribityllumazine synthase
fd: 6,7-dimethyl-8-ribityllumazine synthase
gA: 6,7-dimethyl-8-ribityllumazine synthase
gB: 6,7-dimethyl-8-ribityllumazine synthase
gC: 6,7-dimethyl-8-ribityllumazine synthase
gD: 6,7-dimethyl-8-ribityllumazine synthase
ga: 6,7-dimethyl-8-ribityllumazine synthase
gb: 6,7-dimethyl-8-ribityllumazine synthase
gc: 6,7-dimethyl-8-ribityllumazine synthase
gd: 6,7-dimethyl-8-ribityllumazine synthase
hA: 6,7-dimethyl-8-ribityllumazine synthase
hB: 6,7-dimethyl-8-ribityllumazine synthase
hC: 6,7-dimethyl-8-ribityllumazine synthase
hD: 6,7-dimethyl-8-ribityllumazine synthase
ha: 6,7-dimethyl-8-ribityllumazine synthase
hb: 6,7-dimethyl-8-ribityllumazine synthase
hc: 6,7-dimethyl-8-ribityllumazine synthase
hd: 6,7-dimethyl-8-ribityllumazine synthase
iA: 6,7-dimethyl-8-ribityllumazine synthase
iB: 6,7-dimethyl-8-ribityllumazine synthase
iC: 6,7-dimethyl-8-ribityllumazine synthase
iD: 6,7-dimethyl-8-ribityllumazine synthase
ia: 6,7-dimethyl-8-ribityllumazine synthase
ib: 6,7-dimethyl-8-ribityllumazine synthase
ic: 6,7-dimethyl-8-ribityllumazine synthase
id: 6,7-dimethyl-8-ribityllumazine synthase
jA: 6,7-dimethyl-8-ribityllumazine synthase
jB: 6,7-dimethyl-8-ribityllumazine synthase
jC: 6,7-dimethyl-8-ribityllumazine synthase
jD: 6,7-dimethyl-8-ribityllumazine synthase
ja: 6,7-dimethyl-8-ribityllumazine synthase
jb: 6,7-dimethyl-8-ribityllumazine synthase
jc: 6,7-dimethyl-8-ribityllumazine synthase
jd: 6,7-dimethyl-8-ribityllumazine synthase
kA: 6,7-dimethyl-8-ribityllumazine synthase
kB: 6,7-dimethyl-8-ribityllumazine synthase
kC: 6,7-dimethyl-8-ribityllumazine synthase
kD: 6,7-dimethyl-8-ribityllumazine synthase
ka: 6,7-dimethyl-8-ribityllumazine synthase
kb: 6,7-dimethyl-8-ribityllumazine synthase
kc: 6,7-dimethyl-8-ribityllumazine synthase
kd: 6,7-dimethyl-8-ribityllumazine synthase
lA: 6,7-dimethyl-8-ribityllumazine synthase
lB: 6,7-dimethyl-8-ribityllumazine synthase
lC: 6,7-dimethyl-8-ribityllumazine synthase
lD: 6,7-dimethyl-8-ribityllumazine synthase
la: 6,7-dimethyl-8-ribityllumazine synthase
lb: 6,7-dimethyl-8-ribityllumazine synthase
lc: 6,7-dimethyl-8-ribityllumazine synthase
ld: 6,7-dimethyl-8-ribityllumazine synthase
mA: 6,7-dimethyl-8-ribityllumazine synthase
mB: 6,7-dimethyl-8-ribityllumazine synthase
mC: 6,7-dimethyl-8-ribityllumazine synthase
mD: 6,7-dimethyl-8-ribityllumazine synthase
ma: 6,7-dimethyl-8-ribityllumazine synthase
mb: 6,7-dimethyl-8-ribityllumazine synthase
mc: 6,7-dimethyl-8-ribityllumazine synthase
md: 6,7-dimethyl-8-ribityllumazine synthase
nA: 6,7-dimethyl-8-ribityllumazine synthase
nB: 6,7-dimethyl-8-ribityllumazine synthase
nC: 6,7-dimethyl-8-ribityllumazine synthase
nD: 6,7-dimethyl-8-ribityllumazine synthase
na: 6,7-dimethyl-8-ribityllumazine synthase
nb: 6,7-dimethyl-8-ribityllumazine synthase
nc: 6,7-dimethyl-8-ribityllumazine synthase
nd: 6,7-dimethyl-8-ribityllumazine synthase
oA: 6,7-dimethyl-8-ribityllumazine synthase
oB: 6,7-dimethyl-8-ribityllumazine synthase
oC: 6,7-dimethyl-8-ribityllumazine synthase
oD: 6,7-dimethyl-8-ribityllumazine synthase
oa: 6,7-dimethyl-8-ribityllumazine synthase
ob: 6,7-dimethyl-8-ribityllumazine synthase
oc: 6,7-dimethyl-8-ribityllumazine synthase
od: 6,7-dimethyl-8-ribityllumazine synthase
pA: 6,7-dimethyl-8-ribityllumazine synthase
pB: 6,7-dimethyl-8-ribityllumazine synthase
pC: 6,7-dimethyl-8-ribityllumazine synthase
pD: 6,7-dimethyl-8-ribityllumazine synthase
pa: 6,7-dimethyl-8-ribityllumazine synthase
pb: 6,7-dimethyl-8-ribityllumazine synthase
pc: 6,7-dimethyl-8-ribityllumazine synthase
pd: 6,7-dimethyl-8-ribityllumazine synthase
qA: 6,7-dimethyl-8-ribityllumazine synthase
qB: 6,7-dimethyl-8-ribityllumazine synthase
qC: 6,7-dimethyl-8-ribityllumazine synthase
qD: 6,7-dimethyl-8-ribityllumazine synthase
qa: 6,7-dimethyl-8-ribityllumazine synthase
qb: 6,7-dimethyl-8-ribityllumazine synthase
qc: 6,7-dimethyl-8-ribityllumazine synthase
qd: 6,7-dimethyl-8-ribityllumazine synthase
rA: 6,7-dimethyl-8-ribityllumazine synthase
rB: 6,7-dimethyl-8-ribityllumazine synthase
rC: 6,7-dimethyl-8-ribityllumazine synthase
rD: 6,7-dimethyl-8-ribityllumazine synthase
ra: 6,7-dimethyl-8-ribityllumazine synthase
rb: 6,7-dimethyl-8-ribityllumazine synthase
rc: 6,7-dimethyl-8-ribityllumazine synthase
rd: 6,7-dimethyl-8-ribityllumazine synthase
sA: 6,7-dimethyl-8-ribityllumazine synthase
sB: 6,7-dimethyl-8-ribityllumazine synthase
sC: 6,7-dimethyl-8-ribityllumazine synthase
sD: 6,7-dimethyl-8-ribityllumazine synthase
sa: 6,7-dimethyl-8-ribityllumazine synthase
sb: 6,7-dimethyl-8-ribityllumazine synthase
sc: 6,7-dimethyl-8-ribityllumazine synthase
sd: 6,7-dimethyl-8-ribityllumazine synthase
tA: 6,7-dimethyl-8-ribityllumazine synthase
tB: 6,7-dimethyl-8-ribityllumazine synthase
tC: 6,7-dimethyl-8-ribityllumazine synthase
tD: 6,7-dimethyl-8-ribityllumazine synthase
ta: 6,7-dimethyl-8-ribityllumazine synthase
tb: 6,7-dimethyl-8-ribityllumazine synthase
tc: 6,7-dimethyl-8-ribityllumazine synthase
td: 6,7-dimethyl-8-ribityllumazine synthase
uA: 6,7-dimethyl-8-ribityllumazine synthase
uB: 6,7-dimethyl-8-ribityllumazine synthase
uC: 6,7-dimethyl-8-ribityllumazine synthase
uD: 6,7-dimethyl-8-ribityllumazine synthase
ua: 6,7-dimethyl-8-ribityllumazine synthase
ub: 6,7-dimethyl-8-ribityllumazine synthase
uc: 6,7-dimethyl-8-ribityllumazine synthase
ud: 6,7-dimethyl-8-ribityllumazine synthase
vA: 6,7-dimethyl-8-ribityllumazine synthase
vB: 6,7-dimethyl-8-ribityllumazine synthase
vC: 6,7-dimethyl-8-ribityllumazine synthase
vD: 6,7-dimethyl-8-ribityllumazine synthase
va: 6,7-dimethyl-8-ribityllumazine synthase
vb: 6,7-dimethyl-8-ribityllumazine synthase
vc: 6,7-dimethyl-8-ribityllumazine synthase
vd: 6,7-dimethyl-8-ribityllumazine synthase
wA: 6,7-dimethyl-8-ribityllumazine synthase
wB: 6,7-dimethyl-8-ribityllumazine synthase
wC: 6,7-dimethyl-8-ribityllumazine synthase
wD: 6,7-dimethyl-8-ribityllumazine synthase
wa: 6,7-dimethyl-8-ribityllumazine synthase
wb: 6,7-dimethyl-8-ribityllumazine synthase
wc: 6,7-dimethyl-8-ribityllumazine synthase
wd: 6,7-dimethyl-8-ribityllumazine synthase
xA: 6,7-dimethyl-8-ribityllumazine synthase
xB: 6,7-dimethyl-8-ribityllumazine synthase
xC: 6,7-dimethyl-8-ribityllumazine synthase
xD: 6,7-dimethyl-8-ribityllumazine synthase
xa: 6,7-dimethyl-8-ribityllumazine synthase
xb: 6,7-dimethyl-8-ribityllumazine synthase
xc: 6,7-dimethyl-8-ribityllumazine synthase
xd: 6,7-dimethyl-8-ribityllumazine synthase
yA: 6,7-dimethyl-8-ribityllumazine synthase
yB: 6,7-dimethyl-8-ribityllumazine synthase
yC: 6,7-dimethyl-8-ribityllumazine synthase
yD: 6,7-dimethyl-8-ribityllumazine synthase
ya: 6,7-dimethyl-8-ribityllumazine synthase
yb: 6,7-dimethyl-8-ribityllumazine synthase
yc: 6,7-dimethyl-8-ribityllumazine synthase
yd: 6,7-dimethyl-8-ribityllumazine synthase
zA: 6,7-dimethyl-8-ribityllumazine synthase
zB: 6,7-dimethyl-8-ribityllumazine synthase
zC: 6,7-dimethyl-8-ribityllumazine synthase
zD: 6,7-dimethyl-8-ribityllumazine synthase
za: 6,7-dimethyl-8-ribityllumazine synthase
zb: 6,7-dimethyl-8-ribityllumazine synthase
zc: 6,7-dimethyl-8-ribityllumazine synthase
zd: 6,7-dimethyl-8-ribityllumazine synthase


Theoretical massNumber of molelcules
Total (without water)5,203,570480
Polymers5,203,570480
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein ...
6,7-dimethyl-8-ribityllumazine synthase / DMRL synthase / LS / Lumazine synthase


Mass: 12324.837 Da / Num. of mol.: 240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: ribH, aq_132 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O66529, 6,7-dimethyl-8-ribityllumazine synthase
#2: Protein ...
6,7-dimethyl-8-ribityllumazine synthase / DMRL synthase / LS / Lumazine synthase


Mass: 9356.705 Da / Num. of mol.: 240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: ribH, aq_132 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O66529, 6,7-dimethyl-8-ribityllumazine synthase
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1Nucleocapsid NC-4COMPLEXEvolved and split variant of a virus-inspired nucleocapsid design based on the Aquifex aeolicus riboflavin synthaseall0MULTIPLE SOURCES
2Nucleocapsid NC-4, N-terminal segmentsCOMPLEX1RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11
22NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia virus lambda10710
22Aquifex aeolicus VF5 (bacteria)224324
32Aquifex aeolicus VF5 (bacteria)224324
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli BL21(DE3) (bacteria)469008
22Escherichia coli BL21(DE3) (bacteria)469008
32Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 22 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7PHENIX1.18model fitting
8UCSF ChimeraChimeraX 0.91model fitting
9PyMOL2.1.1model fitting
11RELION3initial Euler assignment
12RELION3final Euler assignment
13RELION3classification
14RELION33D reconstruction
15PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 69723
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20021 / Symmetry type: POINT
Atomic model buildingB value: 66.9 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 1HQK

1hqk


Pdb chain-ID: A / Accession code: 1HQK / Source name: PDB / Type: experimental model

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