[English] 日本語
Yorodumi
- EMDB-1700: Negative stain EM structure of human native COP9 Signalosome (CSN) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1700
TitleNegative stain EM structure of human native COP9 Signalosome (CSN)
Map dataApo CSN map
Sample
  • Sample: Human erythrocyte COP9 Signalosome
  • Protein or peptide: Cop9 Signalosome
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsEnchev R / Schreiber A / Beuron F / Morris E
CitationJournal: Structure / Year: 2010
Title: Structural insights into the COP9 signalosome and its common architecture with the 26S proteasome lid and eIF3.
Authors: Radoslav I Enchev / Anne Schreiber / Fabienne Beuron / Edward P Morris /
Abstract: The evolutionary conserved COP9 signalosome (CSN), a large multisubunit complex, plays a central role in regulating ubiquitination and cell signaling. Here we report recombinant insect cell ...The evolutionary conserved COP9 signalosome (CSN), a large multisubunit complex, plays a central role in regulating ubiquitination and cell signaling. Here we report recombinant insect cell expression and two-step purification of human CSN and demonstrate its functional assembly. We further obtain a three-dimensional structure of both native and recombinant CSN using electron microscopy and single particle analysis. Antibody labeling of CSN5 and segmentation of the structure suggest a likely subunit distribution and the architecture of its helical repeat subunits is revealed. We compare the structure of CSN with its homologous complexes, the 26S proteasome lid and eIF3, and propose a conserved architecture implying similar assembly pathways and/or conserved substrate interaction modes.
History
DepositionFeb 8, 2010-
Header (metadata) releaseMay 13, 2010-
Map releaseMay 13, 2010-
UpdateMay 13, 2010-
Current statusMay 13, 2010Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1700.jpg

Downloads & links

-
Map

FileDownload / File: emd_1700.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApo CSN map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.47 Å/pix.
x 128 pix.
= 444.16 Å		3.47 Å/pix.
x 128 pix.
= 444.16 Å		3.47 Å/pix.
x 128 pix.
= 444.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.47 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.00891048 - 0.245599
Average (Standard dev.)0.000351193 (±0.00567995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-63-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 444.16 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.473.473.47
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z444.160444.160444.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS-64-63-64
NC/NR/NS128128128
D min/max/mean-0.0090.2460.000

-
Supplemental data

-
Sample components

-
Entire : Human erythrocyte COP9 Signalosome

EntireName: Human erythrocyte COP9 Signalosome
Components
  • Sample: Human erythrocyte COP9 Signalosome
  • Protein or peptide: Cop9 Signalosome

-
Supramolecule #1000: Human erythrocyte COP9 Signalosome

SupramoleculeName: Human erythrocyte COP9 Signalosome / type: sample / ID: 1000 / Oligomeric state: Heterooctamer / Number unique components: 1
Molecular weightExperimental: 321 KDa / Theoretical: 321 KDa / Method: Native mass spectrometry

-
Macromolecule #1: Cop9 Signalosome

MacromoleculeName: Cop9 Signalosome / type: protein_or_peptide / ID: 1 / Name.synonym: CSN / Number of copies: 1 / Oligomeric state: Octamer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: Erythrocytes / Location in cell: Nucleus

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.8
Details: 15 mM HEPES pH 7.8, 200 mM NaCl, 1% glycerol and 2 mM DTT
StainingType: NEGATIVE
Details: Sample was applied to glow-discharged quantifoil grids coated with thin carbon, washed with buffer and stained with 2% uranyl acetate
GridDetails: Quantifoil 400 mesh R2/2
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Digitization - Sampling interval: 3.47 µm / Average electron dose: 100 e/Å2
Details: Initial selection was made manually from more than 100 2048x2048 CCD frames
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, SPIDER, EMAN / Number images used: 7877

+
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