[English] 日本語
Yorodumi
- EMDB-3302: Structure of the Salipro-POT complex at 6.48 A -

+
Open data


ID or keywords:

Loading...

-
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 / membrane / identical protein binding
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

-
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

-
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
Voxel sizeX=Y=Z: 1.2156 Å
Density
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

-
Supplemental data

-
Supplemental map: EMD-3302 masked.map

FileEMD-3302_masked.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Supplemental map: half1 unfil.map

Filehalf1_unfil.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Supplemental map: half2 unfil.map

Filehalf2_unfil.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Salipro-POT

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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 41132 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 0.0026 µm / Nominal defocus min: 0.0018 µm / Nominal magnification: 31000
Sample stageSpecimen holder model: OTHER
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
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

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
DetailsProcessed with Relion 1.3

-
Atomic model buiding 1

Initial modelPDB ID:

4lep

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more