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- EMDB-3302: Structure of the Salipro-POT complex at 6.48 A -

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Basic information

Entry
Database: EMDB / ID: EMD-3302
TitleStructure of the Salipro-POT complex at 6.48 A
Map dataReconstruction of Salipro-POT
Sample
  • Sample: Salipro-POT
  • Protein or peptide: Proton-coupled oligopeptide transporter
KeywordsPOT / 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 / identical protein binding / plasma membrane
Similarity search - Function
: / Dipeptide/tripeptide permease / Proton-dependent oligopeptide transporter family / POT family / MFS transporter superfamily
Similarity search - Domain/homology
Proton:oligopeptide symporter POT family
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.48 Å
AuthorsFrauenfeld 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
CitationJournal: 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
DepositionJan 19, 2016-
Header (metadata) releaseMar 2, 2016-
Map releaseMar 2, 2016-
UpdateMar 2, 2016-
Current statusMar 2, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view with section colored by density value
  • Surface level: 3.9
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3302.png

Downloads & links

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Map

FileDownload / File: emd_3302.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Salipro-POT
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 256 pix.
= 311.194 Å		1.22 Å/pix.
x 256 pix.
= 311.194 Å		1.22 Å/pix.
x 256 pix.
= 311.194 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.9 / Movie #1: 3.9
Minimum - Maximum-2.56848264 - 13.579756740000001
Average (Standard dev.)0.00000001 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 311.1936 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21560156251.21560156251.2156015625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z311.194311.194311.194
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.56813.5800.000

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Supplemental data

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Supplemental map: emd 3302 additional 1.map

Fileemd_3302_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 3302 half map 1.map

Fileemd_3302_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 3302 half map 2.map

Fileemd_3302_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Salipro-POT

EntireName: Salipro-POT
Components
  • Sample: Salipro-POT
  • Protein or peptide: Proton-coupled oligopeptide transporter

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Supramolecule #1000: Salipro-POT

SupramoleculeName: Salipro-POT / type: sample / ID: 1000 / Oligomeric state: One tetramer / Number unique components: 1
Molecular weightExperimental: 224 MDa / Theoretical: 250 MDa

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Macromolecule #1: Proton-coupled oligopeptide transporter

MacromoleculeName: Proton-coupled oligopeptide transporter / type: protein_or_peptide / ID: 1 / Name.synonym: PeptTSo2, / Number of copies: 1 / Oligomeric state: Tetramer / Recombinant expression: Yes
Source (natural)Organism: Shewanella oneidensis (bacteria)
Molecular weightExperimental: 224 MDa / Theoretical: 250 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Proton:oligopeptide symporter POT family

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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

Concentration0.7 mg/mL
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 6 before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
DateSep 15, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 288 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsProcessed with Relion 1.3
CTF correctionDetails: each particle
Final reconstructionApplied 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

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Atomic model buiding 1

Initial modelPDB ID:

4lep

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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