+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3538 | |||||||||
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Title | Cryo-EM reconstruction of AaLS-wt | |||||||||
Map data | Cryo-EM map of AaLS-wt | |||||||||
Sample |
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Keywords | cryo-EM / protein cage / dodecahedron / lumazine synthase / Transferase | |||||||||
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 | |||||||||
Biological species | Aquifex aeolicus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Sasaki E / Boehringer D | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3538.map.gz | 5.6 MB | EMDB map data format | |
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Header (meta data) | emd-3538-v30.xml emd-3538.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_3538.png | 100 KB | ||
Filedesc metadata | emd-3538.cif.gz | 4.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3538 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3538 | HTTPS FTP |
-Validation report
Summary document | emd_3538_validation.pdf.gz | 495.5 KB | Display | EMDB validaton report |
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Full document | emd_3538_full_validation.pdf.gz | 495.1 KB | Display | |
Data in XML | emd_3538_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | emd_3538_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3538 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3538 | HTTPS FTP |
-Related structure data
Related structure data | 5mppMC 3543C 3544C 5mq3C 5mq7C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3538.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of AaLS-wt | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : AaLS-wt
Entire | Name: AaLS-wt |
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Components |
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-Supramolecule #1: AaLS-wt
Supramolecule | Name: AaLS-wt / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Aquifex aeolicus (bacteria) |
-Macromolecule #1: 6,7-dimethyl-8-ribityllumazine synthase
Macromolecule | Name: 6,7-dimethyl-8-ribityllumazine synthase / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase |
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Source (natural) | Organism: Aquifex aeolicus (bacteria) |
Molecular weight | Theoretical: 16.728186 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MEIYEGKLTA EGLRFGIVAS RFNHALVDRL VEGAIDCIVR HGGREEDITL VRVPGSWEIP VAAGELARKE DIDAVIAIGV LIRGATPHF DYIASEVSKG LANLSLELRK PITFGVITAD TLEQAIERAG TKHGNKGWEA ALSAIEMANL FKSLR UniProtKB: 6,7-dimethyl-8-ribityllumazine synthase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 4.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |