[English] 日本語
Yorodumi
- EMDB-2264: negative stain single-particle reconstruction of conformation XVI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2264
Titlenegative stain single-particle reconstruction of conformation XVII of the Ltn1 E3 ubiquitin Ligase
Map dataconformational snapshot XVII of Ltn1
Sample
  • Sample: snapshot XVII of Ltn1 conformer
  • Protein or peptide: Ltn1
Keywordsconformational heterogeneity / Ltn1/Listerin / RING E3 ubiquitin ligase / translational surveillance / neurodegenerative disease
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 45.8 Å
AuthorsLyumkis D / Doamekpor SK / Bengtson MH / Lee JW / Toro TB / Petroski MD / Lima CD / Potter CS / Carragher B / Joazeiro CAP
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Single-particle EM reveals extensive conformational variability of the Ltn1 E3 ligase.
Authors: Dmitry Lyumkis / Selom K Doamekpor / Mario H Bengtson / Joong-Won Lee / Tasha B Toro / Matthew D Petroski / Christopher D Lima / Clinton S Potter / Bridget Carragher / Claudio A P Joazeiro /
Abstract: Ltn1 is a 180-kDa E3 ubiquitin ligase that associates with ribosomes and marks certain aberrant, translationally arrested nascent polypeptide chains for proteasomal degradation. In addition to its ...Ltn1 is a 180-kDa E3 ubiquitin ligase that associates with ribosomes and marks certain aberrant, translationally arrested nascent polypeptide chains for proteasomal degradation. In addition to its evolutionarily conserved large size, Ltn1 is characterized by the presence of a conserved N terminus, HEAT/ARM repeats predicted to comprise the majority of the protein, and a C-terminal catalytic RING domain, although the protein's exact structure is unknown. We used numerous single-particle EM strategies to characterize Ltn1's structure based on negative stain and vitreous ice data. Two-dimensional classifications and subsequent 3D reconstructions of electron density maps show that Ltn1 has an elongated form and presents a continuum of conformational states about two flexible hinge regions, whereas its overall architecture is reminiscent of multisubunit cullin-RING ubiquitin ligase complexes. We propose a model of Ltn1 function based on its conformational variability and flexibility that describes how these features may play a role in cotranslational protein quality control.
History
DepositionDec 25, 2012-
Header (metadata) releaseJan 16, 2013-
Map releaseJan 16, 2013-
UpdateJul 3, 2013-
Current statusJul 3, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2264.png

Downloads & links

-
Map

FileDownload / File: emd_2264.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconformational snapshot XVII of Ltn1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 160 pix.
= 348.8 Å		2.18 Å/pix.
x 160 pix.
= 348.8 Å		2.18 Å/pix.
x 160 pix.
= 348.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-1.42925966 - 2.55422163
Average (Standard dev.)-0.00311261 (±0.15115072)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 348.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.182.182.18
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z348.800348.800348.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-1.4292.554-0.003

-
Supplemental data

-
Sample components

-
Entire : snapshot XVII of Ltn1 conformer

EntireName: snapshot XVII of Ltn1 conformer
Components
  • Sample: snapshot XVII of Ltn1 conformer
  • Protein or peptide: Ltn1

-
Supramolecule #1000: snapshot XVII of Ltn1 conformer

SupramoleculeName: snapshot XVII of Ltn1 conformer / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 180 MDa / Theoretical: 180 MDa / Method: SDS-PAGE

-
Macromolecule #1: Ltn1

MacromoleculeName: Ltn1 / type: protein_or_peptide / ID: 1 / Name.synonym: Listerin / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
Molecular weightExperimental: 180 MDa / Theoretical: 180 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.01 mg/mL
BufferpH: 8 / Details: 190 mM NaCl, 20 mM Tris, 1mM BME
StainingType: NEGATIVE
Details: 3 microliters of sample at a concentration of 0.01 mg/mL was applied to a C-flat grid with 2-micron-diameter holes overlaid by thin 1.5 nm continuous carbon. The specimen was stained with 2% ...Details: 3 microliters of sample at a concentration of 0.01 mg/mL was applied to a C-flat grid with 2-micron-diameter holes overlaid by thin 1.5 nm continuous carbon. The specimen was stained with 2% uranyl formate 3 times, then let air-dry.
GridDetails: c-flat grids overlaid with thin (~1.5 nm) carbon
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 298 K
DateMar 23, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 489 / Average electron dose: 15 e/Å2
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 50000
Sample stageSpecimen holder: single-tilt room temperature / Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle min: -55
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Detailsrandom-conical tilt reconstruction
CTF correctionDetails: each micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 45.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider, Appion / Number images used: 377
Final two d classificationNumber classes: 1

+
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