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- PDB-5mq3: Structure of AaLS-neg -

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Basic information

Entry
Database: PDB / ID: 5mq3
TitleStructure of AaLS-neg
Components6,7-dimethyl-8-ribityllumazine synthase
KeywordsTRANSFERASE / cryo-EM / porous protein cage / tetrahedral symmetry / engineered lumazine synthase
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: 5.4 Å
AuthorsSasaki, E. / Boehringer, D. / Leibundgut, M. / Ban, N. / Hilvert, D.
Funding support1items
OrganizationGrant numberCountry
European Research CouncilERC-dG-2012-321295
CitationJournal: Nat Commun / Year: 2017
Title: Structure and assembly of scalable porous protein cages.
Authors: Eita Sasaki / Daniel Böhringer / Michiel van de Waterbeemd / Marc Leibundgut / Reinhard Zschoche / Albert J R Heck / Nenad Ban / Donald Hilvert /
Abstract: Proteins that self-assemble into regular shell-like polyhedra are useful, both in nature and in the laboratory, as molecular containers. Here we describe cryo-electron microscopy (EM) structures of ...Proteins that self-assemble into regular shell-like polyhedra are useful, both in nature and in the laboratory, as molecular containers. Here we describe cryo-electron microscopy (EM) structures of two versatile encapsulation systems that exploit engineered electrostatic interactions for cargo loading. We show that increasing the number of negative charges on the lumenal surface of lumazine synthase, a protein that naturally assembles into a ∼1-MDa dodecahedron composed of 12 pentamers, induces stepwise expansion of the native protein shell, giving rise to thermostable ∼3-MDa and ∼6-MDa assemblies containing 180 and 360 subunits, respectively. Remarkably, these expanded particles assume unprecedented tetrahedrally and icosahedrally symmetric structures constructed entirely from pentameric units. Large keyhole-shaped pores in the shell, not present in the wild-type capsid, enable diffusion-limited encapsulation of complementarily charged guests. The structures of these supercharged assemblies demonstrate how programmed electrostatic effects can be effectively harnessed to tailor the architecture and properties of protein cages.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
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
AE: 6,7-dimethyl-8-ribityllumazine synthase
AF: 6,7-dimethyl-8-ribityllumazine synthase
AG: 6,7-dimethyl-8-ribityllumazine synthase
AH: 6,7-dimethyl-8-ribityllumazine synthase
AI: 6,7-dimethyl-8-ribityllumazine synthase
AJ: 6,7-dimethyl-8-ribityllumazine synthase
AK: 6,7-dimethyl-8-ribityllumazine synthase
AL: 6,7-dimethyl-8-ribityllumazine synthase
AM: 6,7-dimethyl-8-ribityllumazine synthase
AN: 6,7-dimethyl-8-ribityllumazine synthase
AO: 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
BE: 6,7-dimethyl-8-ribityllumazine synthase
BF: 6,7-dimethyl-8-ribityllumazine synthase
BG: 6,7-dimethyl-8-ribityllumazine synthase
BH: 6,7-dimethyl-8-ribityllumazine synthase
BI: 6,7-dimethyl-8-ribityllumazine synthase
BJ: 6,7-dimethyl-8-ribityllumazine synthase
BK: 6,7-dimethyl-8-ribityllumazine synthase
BL: 6,7-dimethyl-8-ribityllumazine synthase
BM: 6,7-dimethyl-8-ribityllumazine synthase
BN: 6,7-dimethyl-8-ribityllumazine synthase
BO: 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
CE: 6,7-dimethyl-8-ribityllumazine synthase
CF: 6,7-dimethyl-8-ribityllumazine synthase
CG: 6,7-dimethyl-8-ribityllumazine synthase
CH: 6,7-dimethyl-8-ribityllumazine synthase
CI: 6,7-dimethyl-8-ribityllumazine synthase
CJ: 6,7-dimethyl-8-ribityllumazine synthase
CK: 6,7-dimethyl-8-ribityllumazine synthase
CL: 6,7-dimethyl-8-ribityllumazine synthase
CM: 6,7-dimethyl-8-ribityllumazine synthase
CN: 6,7-dimethyl-8-ribityllumazine synthase
CO: 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
DE: 6,7-dimethyl-8-ribityllumazine synthase
DF: 6,7-dimethyl-8-ribityllumazine synthase
DG: 6,7-dimethyl-8-ribityllumazine synthase
DH: 6,7-dimethyl-8-ribityllumazine synthase
DI: 6,7-dimethyl-8-ribityllumazine synthase
DJ: 6,7-dimethyl-8-ribityllumazine synthase
DK: 6,7-dimethyl-8-ribityllumazine synthase
DL: 6,7-dimethyl-8-ribityllumazine synthase
DM: 6,7-dimethyl-8-ribityllumazine synthase
DN: 6,7-dimethyl-8-ribityllumazine synthase
DO: 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
EE: 6,7-dimethyl-8-ribityllumazine synthase
EF: 6,7-dimethyl-8-ribityllumazine synthase
EG: 6,7-dimethyl-8-ribityllumazine synthase
EH: 6,7-dimethyl-8-ribityllumazine synthase
EI: 6,7-dimethyl-8-ribityllumazine synthase
EJ: 6,7-dimethyl-8-ribityllumazine synthase
EK: 6,7-dimethyl-8-ribityllumazine synthase
EL: 6,7-dimethyl-8-ribityllumazine synthase
EM: 6,7-dimethyl-8-ribityllumazine synthase
EN: 6,7-dimethyl-8-ribityllumazine synthase
EO: 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
FE: 6,7-dimethyl-8-ribityllumazine synthase
FF: 6,7-dimethyl-8-ribityllumazine synthase
FG: 6,7-dimethyl-8-ribityllumazine synthase
FH: 6,7-dimethyl-8-ribityllumazine synthase
FI: 6,7-dimethyl-8-ribityllumazine synthase
FJ: 6,7-dimethyl-8-ribityllumazine synthase
FK: 6,7-dimethyl-8-ribityllumazine synthase
FL: 6,7-dimethyl-8-ribityllumazine synthase
FM: 6,7-dimethyl-8-ribityllumazine synthase
FN: 6,7-dimethyl-8-ribityllumazine synthase
FO: 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
GE: 6,7-dimethyl-8-ribityllumazine synthase
GF: 6,7-dimethyl-8-ribityllumazine synthase
GG: 6,7-dimethyl-8-ribityllumazine synthase
GH: 6,7-dimethyl-8-ribityllumazine synthase
GI: 6,7-dimethyl-8-ribityllumazine synthase
GJ: 6,7-dimethyl-8-ribityllumazine synthase
GK: 6,7-dimethyl-8-ribityllumazine synthase
GL: 6,7-dimethyl-8-ribityllumazine synthase
GM: 6,7-dimethyl-8-ribityllumazine synthase
GN: 6,7-dimethyl-8-ribityllumazine synthase
GO: 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
HE: 6,7-dimethyl-8-ribityllumazine synthase
HF: 6,7-dimethyl-8-ribityllumazine synthase
HG: 6,7-dimethyl-8-ribityllumazine synthase
HH: 6,7-dimethyl-8-ribityllumazine synthase
HI: 6,7-dimethyl-8-ribityllumazine synthase
HJ: 6,7-dimethyl-8-ribityllumazine synthase
HK: 6,7-dimethyl-8-ribityllumazine synthase
HL: 6,7-dimethyl-8-ribityllumazine synthase
HM: 6,7-dimethyl-8-ribityllumazine synthase
HN: 6,7-dimethyl-8-ribityllumazine synthase
HO: 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
IE: 6,7-dimethyl-8-ribityllumazine synthase
IF: 6,7-dimethyl-8-ribityllumazine synthase
IG: 6,7-dimethyl-8-ribityllumazine synthase
IH: 6,7-dimethyl-8-ribityllumazine synthase
II: 6,7-dimethyl-8-ribityllumazine synthase
IJ: 6,7-dimethyl-8-ribityllumazine synthase
IK: 6,7-dimethyl-8-ribityllumazine synthase
IL: 6,7-dimethyl-8-ribityllumazine synthase
IM: 6,7-dimethyl-8-ribityllumazine synthase
IN: 6,7-dimethyl-8-ribityllumazine synthase
IO: 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
JE: 6,7-dimethyl-8-ribityllumazine synthase
JF: 6,7-dimethyl-8-ribityllumazine synthase
JG: 6,7-dimethyl-8-ribityllumazine synthase
JH: 6,7-dimethyl-8-ribityllumazine synthase
JI: 6,7-dimethyl-8-ribityllumazine synthase
JJ: 6,7-dimethyl-8-ribityllumazine synthase
JK: 6,7-dimethyl-8-ribityllumazine synthase
JL: 6,7-dimethyl-8-ribityllumazine synthase
JM: 6,7-dimethyl-8-ribityllumazine synthase
JN: 6,7-dimethyl-8-ribityllumazine synthase
JO: 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
KE: 6,7-dimethyl-8-ribityllumazine synthase
KF: 6,7-dimethyl-8-ribityllumazine synthase
KG: 6,7-dimethyl-8-ribityllumazine synthase
KH: 6,7-dimethyl-8-ribityllumazine synthase
KI: 6,7-dimethyl-8-ribityllumazine synthase
KJ: 6,7-dimethyl-8-ribityllumazine synthase
KK: 6,7-dimethyl-8-ribityllumazine synthase
KL: 6,7-dimethyl-8-ribityllumazine synthase
KM: 6,7-dimethyl-8-ribityllumazine synthase
KN: 6,7-dimethyl-8-ribityllumazine synthase
KO: 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
LE: 6,7-dimethyl-8-ribityllumazine synthase
LF: 6,7-dimethyl-8-ribityllumazine synthase
LG: 6,7-dimethyl-8-ribityllumazine synthase
LH: 6,7-dimethyl-8-ribityllumazine synthase
LI: 6,7-dimethyl-8-ribityllumazine synthase
LJ: 6,7-dimethyl-8-ribityllumazine synthase
LK: 6,7-dimethyl-8-ribityllumazine synthase
LL: 6,7-dimethyl-8-ribityllumazine synthase
LM: 6,7-dimethyl-8-ribityllumazine synthase
LN: 6,7-dimethyl-8-ribityllumazine synthase
LO: 6,7-dimethyl-8-ribityllumazine synthase


Theoretical massNumber of molelcules
Total (without water)3,184,221180
Polymers3,184,221180
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
6,7-dimethyl-8-ribityllumazine synthase / Lumazine synthase / AaLS-neg


Mass: 17690.119 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: ribH, aq_132 / Production host: Escherichia coli (E. coli)
References: UniProt: O66529, 6,7-dimethyl-8-ribityllumazine synthase

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: AaLS-neg / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Aquifex aeolicus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: na
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND3CTF correction
5RELION1.4CTF correction
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
13RELION1.4classification
14RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26769 / Symmetry type: POINT

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