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- PDB-7a4i: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-3 -

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Basic information

Entry
Database: PDB / ID: 7a4i
TitleAquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-3
ComponentsAntitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
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 / RNA polymerase binding / bacterial-type RNA polymerase core enzyme binding / transcription antitermination factor activity, RNA binding / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination ...6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / RNA polymerase binding / bacterial-type RNA polymerase core enzyme binding / transcription antitermination factor activity, RNA binding / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / RNA stem-loop binding / single-stranded RNA binding / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / cytosol
Similarity search - Function
Antitermination protein N, arginine-rich motif / 36-mer N-terminal peptide of the N protein (N36) / 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 / Antitermination protein N
Similarity search - Component
Biological speciesEscherichia virus lambda
Aquifex aeolicus VF5 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.04 Å
AuthorsTetter, S. / Hilvert, D.
Funding support1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-AdG-2012-321295
Citation
Journal: Science / Year: 2021
Title: Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein.
Authors: Stephan Tetter / Naohiro Terasaka / Angela Steinauer / Richard J Bingham / Sam Clark / Andrew J P Scott / Nikesh Patel / Marc Leibundgut / Emma Wroblewski / Nenad Ban / Peter G Stockley / ...Authors: Stephan Tetter / Naohiro Terasaka / Angela Steinauer / Richard J Bingham / Sam Clark / Andrew J P Scott / Nikesh Patel / Marc Leibundgut / Emma Wroblewski / Nenad Ban / Peter G Stockley / Reidun Twarock / Donald Hilvert /
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 ...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.
#1: Journal: Biorxiv / Year: 2021
Title: Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein
Authors: 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.
History
DepositionAug 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
AA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
AB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
AC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
AD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
BA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
BB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
BC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
BD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
CA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
CB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
CC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
CD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
DA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
DB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
DC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
DD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
EA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
EB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
EC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
ED: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
FA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
FB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
FC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
FD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
GA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
GB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
GC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
GD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
HA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
HB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
HC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
HD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
IA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
IB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
IC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
ID: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
5A: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
5B: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
5C: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
5D: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
JA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
JB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
JC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
JD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
KA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
KB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
KC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
KD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
LA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
LB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
LC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
LD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
MA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
MB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
MC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
MD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
NA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
NB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
NC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
ND: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
OA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
OB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
OC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
OD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
PA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
PB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
PC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
PD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
6A: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
6B: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
6C: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
6D: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
7A: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
7B: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
7C: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
7D: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
QA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
QB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
QC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
QD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
RA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
RB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
RC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
RD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
SA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
SB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
SC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
SD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
TA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
TB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
TC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
TD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
UA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
UB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
UC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
UD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
VA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
VB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
VC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
VD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
WA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
WB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
WC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
WD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
XA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
XB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
XC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
XD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
YA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
YB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
YC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
YD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
ZA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
ZB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
ZC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
ZD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
aA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
aB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
aC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
aD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
bA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
bB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
bC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
bD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
cA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
cB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
cC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
cD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
dA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
dB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
dC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
dD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
eA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
eB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
eC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
eD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
fA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
fB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
fC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
fD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
gA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
gB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
gC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
gD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
hA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
hB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
hC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
hD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
iA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
iB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
iC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
iD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
jA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
jB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
jC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
jD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
kA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
kB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
kC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
kD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
lA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
lB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
lC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
lD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
mA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
mB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
mC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
mD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
nA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
nB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
nC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
nD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
oA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
oB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
oC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
oD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
pA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
pB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
pC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
pD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
qA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
qB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
qC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
qD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
rA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
rB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
rC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
rD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
sA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
sB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
sC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
sD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
tA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
tB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
tC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
tD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
uA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
uB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
uC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
uD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
vA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
vB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
vC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
vD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
wA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
wB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
wC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
wD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
xA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
xB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
xC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
xD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
yA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
yB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
yC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
yD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
zA: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
zB: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
zC: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
zD: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
0A: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
0B: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
0C: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
0D: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
1A: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
1B: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
1C: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
1D: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
2A: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
2B: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
2C: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
2D: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
3A: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
3B: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
3C: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
3D: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
4A: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
4B: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
4C: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
4D: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase


Theoretical massNumber of molelcules
Total (without water)5,160,554240
Polymers5,160,554240
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase / Regulatory protein N / PN / Lumazine synthase / Lumazine synthase


Mass: 21502.309 Da / Num. of mol.: 240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus lambda, (gene. exp.) Aquifex aeolicus VF5 (bacteria)
Gene: N, lambdap49, ribH, aq_132 / Variant: VF5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P03045, UniProt: O66529, 6,7-dimethyl-8-ribityllumazine synthase

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Nucleocapsid NC-3 / Type: CELL
Details: Evolved variant of a virus-inspired nucleocapsid design based on the Aquifex aeolicus riboflavin synthase
Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Escherichia virus lambda10710
21Aquifex aeolicus VF5 (bacteria)224324
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding 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: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 62000 X / Nominal defocus max: 3300 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 35 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 134
Image scansMovie frames/image: 7 / Used frames/image: 1-7

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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: 32411
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 7.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3815 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 550 / Protocol: RIGID BODY FIT / Space: REAL

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