[English] 日本語
Yorodumi
- EMDB-5229: Alternative Oligomeric States of the Yeast Rvb1-Rvb2 Complex Indu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5229
TitleAlternative Oligomeric States of the Yeast Rvb1-Rvb2 Complex Induced by Histidine Tags
Map dataRvb1-Rvb2 complex assembled with non-tagged Rvb1 and His-tagged Rvb2 proteins
Sample
  • Sample: Rvb1-Rvb2 complex assembled with non-tagged Rvb1 and His-tagged Rvb2 proteins
  • Protein or peptide: helicase
KeywordsRvb1 / Rvb2
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsCheung KLY / Huen J / Kakihara Y / Houry WA / Ortega J
CitationJournal: J Mol Biol / Year: 2010
Title: Alternative oligomeric states of the yeast Rvb1/Rvb2 complex induced by histidine tags.
Authors: Kevin L Y Cheung / Jennifer Huen / Yoshito Kakihara / Walid A Houry / Joaquin Ortega /
Abstract: Rvb1 and Rvb2 are essential AAA(+) (ATPases associated with diverse cellular activities) helicases, which are important components of critical complexes such as chromatin remodeling and telomerase ...Rvb1 and Rvb2 are essential AAA(+) (ATPases associated with diverse cellular activities) helicases, which are important components of critical complexes such as chromatin remodeling and telomerase complexes. The oligomeric state of the Rvb proteins has been controversial. Independent studies from several groups have described the yeast and human Rvb1/Rvb2 complex both as a single and as a double hexameric ring complex. We found that histidine-tagged constructs of yeast Rvb proteins employed in some of these studies induced the assembly of double hexameric ring Rvb1/Rvb2 complexes. Instead, untagged versions of these proteins assemble into single hexameric rings. Furthermore, purified endogenous untagged Rvb1/Rvb2 complexes from Saccharomyces cerevisiae were also found as single hexameric rings, similar to the complexes assembled in vitro from the purified untagged components. These results demonstrate that some of the differences between the reported structures are caused by histidine tags and imply that further studies on the purified proteins should be carried out using untagged constructs.
History
DepositionAug 17, 2010-
Header (metadata) releaseAug 24, 2010-
Map releaseNov 17, 2010-
UpdateNov 17, 2010-
Current statusNov 17, 2010Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5229_1.tif

Downloads & links

-
Map

FileDownload / File: emd_5229.map.gz / Format: CCP4 / Size: 5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRvb1-Rvb2 complex assembled with non-tagged Rvb1 and His-tagged Rvb2 proteins
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.54 Å/pix.
x 110 pix.
= 279.4 Å		2.54 Å/pix.
x 110 pix.
= 279.4 Å		2.54 Å/pix.
x 110 pix.
= 279.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.0222893 - 0.0705657
Average (Standard dev.)0.00178395 (±0.00900523)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-55-55-55
Dimensions110110110
Spacing110110110
CellA=B=C: 279.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.542.542.54
M x/y/z110110110
origin x/y/z0.0000.0000.000
length x/y/z279.400279.400279.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-55-55-55
NC/NR/NS110110110
D min/max/mean-0.0220.0710.002

-
Supplemental data

-
Sample components

-
Entire : Rvb1-Rvb2 complex assembled with non-tagged Rvb1 and His-tagged R...

EntireName: Rvb1-Rvb2 complex assembled with non-tagged Rvb1 and His-tagged Rvb2 proteins
Components
  • Sample: Rvb1-Rvb2 complex assembled with non-tagged Rvb1 and His-tagged Rvb2 proteins
  • Protein or peptide: helicase

-
Supramolecule #1000: Rvb1-Rvb2 complex assembled with non-tagged Rvb1 and His-tagged R...

SupramoleculeName: Rvb1-Rvb2 complex assembled with non-tagged Rvb1 and His-tagged Rvb2 proteins
type: sample / ID: 1000 / Oligomeric state: 12 / Number unique components: 2
Molecular weightExperimental: 600 KDa / Theoretical: 600 KDa
Method: Size exclusion chromatography and Blue native polyacrylamide gel electrophoresis

-
Macromolecule #1: helicase

MacromoleculeName: helicase / type: protein_or_peptide / ID: 1 / Name.synonym: Rvb1 and Rvb2 / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Saccharomyces cerevisiae
Molecular weightExperimental: 600 KDa / Theoretical: 600 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pProEx (Rvb1) and p11 (Rvb2)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 25mM Tris, 80mM KCl, 10% glycerol
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 1% w/v uranyl acetate for 1 minute
GridDetails: 400 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeJEOL 2010F
TemperatureAverage: 298.15 K
DetailsImages were taken with FasTem low dose kit
DateApr 2, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 12.7 µm / Number real images: 50 / Average electron dose: 10 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Single-tilt / Specimen holder model: JEOL

-
Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: XMIPP / Number images used: 10000

-
Atomic model buiding 1

Initial modelPDB ID:

2c9o

DetailsProtocol: Rigid body. The AAA domains were docked separately from the insertion domain manually using 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