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- EMDB-3544: Cryo-EM reconstruction of AaLS-13 -

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Basic information

Entry
Database: EMDB / ID: EMD-3544
TitleCryo-EM reconstruction of AaLS-13
Map datacryo-EM map of AaLS-13
Sample
  • Complex: AaLS-13
    • Protein or peptide: 6,7-dimethyl-8-ribityllumazine synthaseLumazine 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsSasaki E / Boehringer D / Leibundgut M / Ban N / Hilvert D
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, 2016-
Header (metadata) releaseJan 25, 2017-
Map releaseMar 22, 2017-
UpdateMar 22, 2017-
Current statusMar 22, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5mq7
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3544.png

Downloads & links

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Map

FileDownload / File: emd_3544.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of AaLS-13
Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.041725438 - 0.13126968
Average (Standard dev.)0.0018076668 (±0.008626826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 583.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z583.800583.800583.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.0420.1310.002

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Supplemental data

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Sample components

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Entire : AaLS-13

EntireName: AaLS-13
Components
  • Complex: AaLS-13
    • Protein or peptide: 6,7-dimethyl-8-ribityllumazine synthaseLumazine synthase

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Supramolecule #1: AaLS-13

SupramoleculeName: AaLS-13 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aquifex aeolicus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: 6,7-dimethyl-8-ribityllumazine synthase

MacromoleculeName: 6,7-dimethyl-8-ribityllumazine synthase / type: protein_or_peptide / ID: 1 / Number of copies: 360 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase
Source (natural)Organism: Aquifex aeolicus (bacteria) / Strain: VF5
Molecular weightTheoretical: 17.569855 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEIYEGKLTA EGLRFGIVAS RFNHALVGRL VEGAIDCIVR HGGREEDITL VCVPGSWEIP VAAGELARKE DIDAVIAIGV LIEGAEPHF DYIASEVSKG LANLSLELRK PISFGDITDD ELEEAIECAG TEHGNKGWEA ALSAIEMANL FKSLRLEHHH H H

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 4.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: CTFFIND (ver. 3), RELION (ver. 1.4))
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationSoftware - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 9900
FSC plot (resolution estimation)

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