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Yorodumi- PDB-5kp9: Structure of Nanoparticle Released from Enveloped Protein Nanoparticle -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kp9 | ||||||||||||||||||||||||||||||||||||||||
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Title | Structure of Nanoparticle Released from Enveloped Protein Nanoparticle | ||||||||||||||||||||||||||||||||||||||||
Components | EPN-01*Keywords | STRUCTURAL PROTEIN / protein design / icosahedral assemblies / cell transduction / enveloped viruses / virus assembly / enveloped protein / nanoparticle | Function / homology | Function and homology information viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / lyase activity / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding ...viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / lyase activity / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function Biological species | Thermotoga maritima (bacteria) | Human immunodeficiency virus type 1 group M subtype B Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å | Authors | Votteler, J. / Ogohara, C. / Yi, S. / Hsia, Y. / Natterman, U. / Belnap, D.M. / King, N.P. / Sundquist, W.I. | Funding support | Germany, United States, 5items |
Citation | Journal: Nature / Year: 2016 | Title: Designed proteins induce the formation of nanocage-containing extracellular vesicles. Authors: Jörg Votteler / Cassandra Ogohara / Sue Yi / Yang Hsia / Una Nattermann / David M Belnap / Neil P King / Wesley I Sundquist / Abstract: Complex biological processes are often performed by self-organizing nanostructures comprising multiple classes of macromolecules, such as ribosomes (proteins and RNA) or enveloped viruses (proteins, ...Complex biological processes are often performed by self-organizing nanostructures comprising multiple classes of macromolecules, such as ribosomes (proteins and RNA) or enveloped viruses (proteins, nucleic acids and lipids). Approaches have been developed for designing self-assembling structures consisting of either nucleic acids or proteins, but strategies for engineering hybrid biological materials are only beginning to emerge. Here we describe the design of self-assembling protein nanocages that direct their own release from human cells inside small vesicles in a manner that resembles some viruses. We refer to these hybrid biomaterials as 'enveloped protein nanocages' (EPNs). Robust EPN biogenesis requires protein sequence elements that encode three distinct functions: membrane binding, self-assembly, and recruitment of the endosomal sorting complexes required for transport (ESCRT) machinery. A variety of synthetic proteins with these functional elements induce EPN biogenesis, highlighting the modularity and generality of the design strategy. Biochemical analyses and cryo-electron microscopy reveal that one design, EPN-01, comprises small (~100 nm) vesicles containing multiple protein nanocages that closely match the structure of the designed 60-subunit self-assembling scaffold. EPNs that incorporate the vesicular stomatitis viral glycoprotein can fuse with target cells and deliver their contents, thereby transferring cargoes from one cell to another. These results show how proteins can be programmed to direct the formation of hybrid biological materials that perform complex tasks, and establish EPNs as a class of designed, modular, genetically-encoded nanomaterials that can transfer molecules between cells. History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5kp9.cif.gz | 49 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kp9.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 5kp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kp9_validation.pdf.gz | 780.6 KB | Display | wwPDB validaton report |
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Full document | 5kp9_full_validation.pdf.gz | 781.5 KB | Display | |
Data in XML | 5kp9_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 5kp9_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/5kp9 ftp://data.pdbj.org/pub/pdb/validation_reports/kp/5kp9 | HTTPS FTP |
-Related structure data
Related structure data | 8278MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 30304.920 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria), (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10) Gene: TM_0066, gag / Strain: isolate BH10 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9WXS1, UniProt: P03347 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: EPN-01* / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Thermotoga maritima (bacteria) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293T / Plasmid: EPN-01* |
Buffer solution | pH: 7.5 / Details: Phosphate-buffered saline |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: EPN nanoparticles released from vesicles by detergent treatment (0.75% CHAPS) |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K / Details: 11 second blot, 0 mm offset |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 41911 X / Calibrated defocus min: 700 nm / Calibrated defocus max: 3300 nm / Cs: 2 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Image recording | Electron dose: 2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Details: Electron dose at specimen was not recorded. |
Image scans | Sampling size: 2.5 µm / Width: 7420 / Height: 7676 / Movie frames/image: 60 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 9177 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8573 / Algorithm: FOURIER SPACE / Num. of class averages: 10 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |