+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3302 | |||||||||
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Title | Structure of the Salipro-POT complex at 6.48 A | |||||||||
Map data | Reconstruction of Salipro-POT | |||||||||
Sample |
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Keywords | POT / salipro / lipid / disk / membrane / protein / transporter / peptider | |||||||||
Function / homology | Function and homology information dipeptide transmembrane transport / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / peptide transport / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Shewanella oneidensis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.48 Å | |||||||||
Authors | Frauenfeld J / Loeving R / Armache JP / Sonnen A / Guettou F / Moberg P / Zhu L / Jegerschoeld C / Flayhan A / Briggs J ...Frauenfeld J / Loeving R / Armache JP / Sonnen A / Guettou F / Moberg P / Zhu L / Jegerschoeld C / Flayhan A / Briggs J / Garoff H / Loew C / Cheng Y / Nordlund P | |||||||||
Citation | Journal: Nat Methods / Year: 2016 Title: A saposin-lipoprotein nanoparticle system for membrane proteins. Authors: Jens Frauenfeld / Robin Löving / Jean-Paul Armache / Andreas F-P Sonnen / Fatma Guettou / Per Moberg / Lin Zhu / Caroline Jegerschöld / Ali Flayhan / John A G Briggs / Henrik Garoff / ...Authors: Jens Frauenfeld / Robin Löving / Jean-Paul Armache / Andreas F-P Sonnen / Fatma Guettou / Per Moberg / Lin Zhu / Caroline Jegerschöld / Ali Flayhan / John A G Briggs / Henrik Garoff / Christian Löw / Yifan Cheng / Pär Nordlund / Abstract: A limiting factor in membrane protein research is the ability to solubilize and stabilize such proteins. Detergents are used most often for solubilizing membrane proteins, but they are associated ...A limiting factor in membrane protein research is the ability to solubilize and stabilize such proteins. Detergents are used most often for solubilizing membrane proteins, but they are associated with protein instability and poor compatibility with structural and biophysical studies. Here we present a saposin-lipoprotein nanoparticle system, Salipro, which allows for the reconstitution of membrane proteins in a lipid environment that is stabilized by a scaffold of saposin proteins. We demonstrate the applicability of the method on two purified membrane protein complexes as well as by the direct solubilization and nanoparticle incorporation of a viral membrane protein complex from the virus membrane. Our approach facilitated high-resolution structural studies of the bacterial peptide transporter PeptTSo2 by single-particle cryo-electron microscopy (cryo-EM) and allowed us to stabilize the HIV envelope glycoprotein in a functional state. | |||||||||
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_3302.map.gz | 45.5 MB | EMDB map data format | |
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Header (meta data) | emd-3302-v30.xml emd-3302.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | EMD-3302.png | 763.3 KB | ||
Others | emd_3302_additional_1.map.gz emd_3302_half_map_1.map.gz emd_3302_half_map_2.map.gz | 2.6 MB 45.8 MB 45.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3302 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3302 | HTTPS FTP |
-Validation report
Summary document | emd_3302_validation.pdf.gz | 232.2 KB | Display | EMDB validaton report |
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Full document | emd_3302_full_validation.pdf.gz | 231.3 KB | Display | |
Data in XML | emd_3302_validation.xml.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3302 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3302 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3302.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Salipro-POT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2156 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 3302 additional 1.map
File | emd_3302_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 3302 half map 1.map
File | emd_3302_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 3302 half map 2.map
File | emd_3302_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Salipro-POT
Entire | Name: Salipro-POT |
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Components |
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-Supramolecule #1000: Salipro-POT
Supramolecule | Name: Salipro-POT / type: sample / ID: 1000 / Oligomeric state: One tetramer / Number unique components: 1 |
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Molecular weight | Experimental: 224 MDa / Theoretical: 250 MDa |
-Macromolecule #1: Proton-coupled oligopeptide transporter
Macromolecule | Name: Proton-coupled oligopeptide transporter / type: protein_or_peptide / ID: 1 / Name.synonym: PeptTSo2, / Number of copies: 1 / Oligomeric state: Tetramer / Recombinant expression: Yes |
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Source (natural) | Organism: Shewanella oneidensis (bacteria) |
Molecular weight | Experimental: 224 MDa / Theoretical: 250 MDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Proton:oligopeptide symporter POT family |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 6 before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Sep 15, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 288 / Average electron dose: 10 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 41132 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 0.0026 µm / Nominal defocus min: 0.0018 µm / Nominal magnification: 31000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | Processed with Relion 1.3 |
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CTF correction | Details: each particle |
Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.48 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 9913 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |