[English] 日本語
Yorodumi
- EMDB-5668: 26S proteasome Rpn11AXA Rpn13-delta mutant -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 5668
Title26S proteasome Rpn11AXA Rpn13-delta mutant
Map dataReconstruction of the Rpn11AXA Rpn13-delta yeast 26S proteasome in the absence of substrate
SampleYeast Rpn11AXA Rpn13-delta mutant 26S proteasome:
26S proteasome
Keywords26S proteasome / 19S regulatory particle / Rpn11 / deubiquitination / AAA+ ATPase / protein translocation / cryoEM / UPS
Function / homologyproteasome regulatory particle / Proteasome, subunit alpha/beta
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 9 Å resolution
AuthorsMatyskiela ME / Lander GC / Martin A
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2013
Title: Conformational switching of the 26S proteasome enables substrate degradation.
Authors: Mary E Matyskiela / Gabriel C Lander / Andreas Martin
DateDeposition: May 8, 2013 / Header (metadata) release: May 22, 2013 / Map release: Jun 19, 2013 / Last update: Jul 17, 2013

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_5668.map.gz (map file in CCP4 format, 54001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
2.17 Å/pix.
= 520.8 Å
240 pix
2.17 Å/pix.
= 520.8 Å
240 pix
2.17 Å/pix.
= 520.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.17 Å
Density
Contour Level:2.0 (by author), 2 (movie #1):
Minimum - Maximum-11.60969639 - 15.19638729
Average (Standard dev.)0.01988752 (0.59111792)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin404040
Limit279279279
Spacing240240240
CellA=B=C: 520.80005 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.172.172.17
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z520.800520.800520.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS404040
NC/NR/NS240240240
D min/max/mean-11.61015.1960.020

-
Supplemental data

-
Sample components

-
Entire Yeast Rpn11AXA Rpn13-delta mutant 26S proteasome

EntireName: Yeast Rpn11AXA Rpn13-delta mutant 26S proteasome / Details: mutant proteasome was purified from yeast / Number of components: 1 / Oligomeric State: holoenzyme
MassTheoretical: 1.5 MDa / Experimental: 1.5 MDa / Measured by: Sedimentation

-
Component #1: protein, 26S proteasome

ProteinName: 26S proteasome / a.k.a: proteasome / Oligomeric Details: monomer / Details: Mutant proteasome was purified from yeast / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 1.5 MDa / Experimental: 1.5 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: yAM11
Source (natural)Location in cell: cytoplasm
External referencesInterPro: Proteasome, subunit alpha/beta / Gene Ontology: proteasome regulatory particle

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/ml
Buffer solution: 60mM HEPES, 50mM NaCl, 50mM KCl, 5mM MgCl2, 0.5mM EDTA, 1mM DTT, 2mM ATP, 0.05% NP40
pH: 7.6
Support film400-mesh C-flats, 2 um holes with 2 um spacing (Protochips Inc.)
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 86 K / Humidity: 50 % / Method: Blot 3 seconds with -1 offset

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Sep 10, 2012 / Details: Data acquired with Leginon
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 100000 X (nominal), 100000 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 210,000 times magnification
Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 2500 nm
Specimen HolderHolder: Gatan 626, 70 degree cryoholder / Model: GATAN LIQUID NITROGEN / Temperature: 79 K ( 78 - 80 K)
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 4740

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 80011
Details: 3D reconstruction with EMAN2/SPARX libraries; final alignment of particles with FREALIGN. Sharpened with SPIDER; low-pass filtered to local resolution with BSOFT.
3D reconstructionAlgorithm: Projection matching / Software: EMAN2/SPARX, FREALIGN / CTF correction: each particle
Details: Final map filtered to local resolution using the blocfilt function in Bsoft. Image processing performed in the Appion processing environment.
Resolution: 9 Å / Resolution method: FSC 0.5

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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