[English] 日本語
Yorodumi
- EMDB-2566: Electron cryo-microscopy of yeast mitochondrial large ribosomal s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2566
TitleElectron cryo-microscopy of yeast mitochondrial large ribosomal subunit
Map dataReconstruction of yeast mitochondrial large ribosomal subunit; this map has a mask around the large ribosomal subunit
Sample
  • Sample: Yeast Mitochondrial Large Ribosomal Subunit
  • Complex: Yeast Mitochondrial Large Ribosomal Subunit
Keywordscryo-EM / yeast mitochondrial ribosome
Function / homology
Function and homology information


positive regulation of mitochondrial DNA replication / mitochondrial cytochrome c oxidase assembly / Mitochondrial protein degradation / DNA strand exchange activity / mitochondrial genome maintenance / ribonuclease III activity / mitochondrial large ribosomal subunit / mitochondrial translation / RNA processing / cell redox homeostasis ...positive regulation of mitochondrial DNA replication / mitochondrial cytochrome c oxidase assembly / Mitochondrial protein degradation / DNA strand exchange activity / mitochondrial genome maintenance / ribonuclease III activity / mitochondrial large ribosomal subunit / mitochondrial translation / RNA processing / cell redox homeostasis / ribosome biogenesis / large ribosomal subunit / single-stranded DNA binding / double-stranded RNA binding / transferase activity / cellular response to oxidative stress / large ribosomal subunit rRNA binding / DNA recombination / cytosolic large ribosomal subunit / mitochondrial inner membrane / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / regulation of DNA-templated transcription / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
54S ribosomal protein L8, C-terminal / Ribosomal L27 protein, C-terminal / Ribosomal L27 protein C-terminal domain / 54S ribosomal protein L8 C-terminal domain / Large ribosomal subunit protein uL24m / Ribosomal protein L31, mitochondrial / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L25 / 54S ribosomal protein L15, mitochondrial ...54S ribosomal protein L8, C-terminal / Ribosomal L27 protein, C-terminal / Ribosomal L27 protein C-terminal domain / 54S ribosomal protein L8 C-terminal domain / Large ribosomal subunit protein uL24m / Ribosomal protein L31, mitochondrial / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L25 / 54S ribosomal protein L15, mitochondrial / MRPL25 domain / 54S ribosomal protein L28, mitochondrial / 54S ribosomal protein L3, double-stranded RNA binding domain / Mitochondrial ribosomal protein subunit L20 / Transcriptional regulation of mitochondrial recombination / Mitochondrial ribosomal protein mL59 / Mitochondrial ribosomal protein L31 / 54S ribosomal protein L36, yeast / : / Ribosomal protein L31p, N-terminal / Ribonuclease-III-like / Ribonuclease III domain / : / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / : / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal subunit 39S / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / : / Mitochondrial ribosomal protein L27 / 39S ribosomal protein L46, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L17 signature. / ACP-like superfamily / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L6, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / : / L28p-like / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein
Similarity search - Domain/homology
Large ribosomal subunit protein bL36m / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein mL60 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein mL58 / Large ribosomal subunit protein mL59 / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein mL49 ...Large ribosomal subunit protein bL36m / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein mL60 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein mL58 / Large ribosomal subunit protein mL59 / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein uL6m / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein uL5m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein mL57 / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein bL31m / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL67 / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL13m
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.2 Å
AuthorsAmunts A / Brown A / Bai XC / Llacer JL / Hussain T / Emsley P / Long F / Murshudov G / Scheres SHW / Ramakrishnan V
CitationJournal: Science / Year: 2014
Title: Structure of the yeast mitochondrial large ribosomal subunit.
Authors: Alexey Amunts / Alan Brown / Xiao-Chen Bai / Jose L Llácer / Tanweer Hussain / Paul Emsley / Fei Long / Garib Murshudov / Sjors H W Scheres / V Ramakrishnan /
Abstract: Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single- ...Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single-particle cryo-electron microscopy. The resolution of 3.2 angstroms enabled a nearly complete atomic model to be built de novo and refined, including 39 proteins, 13 of which are unique to mitochondria, as well as expansion segments of mitoribosomal RNA. The structure reveals a new exit tunnel path and architecture, unique elements of the E site, and a putative membrane docking site.
History
DepositionJan 21, 2014-
Header (metadata) releaseJan 29, 2014-
Map releaseApr 9, 2014-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j6b
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j6b
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD_2566.jpg

Downloads & links

-
Map

FileDownload / File: emd_2566.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of yeast mitochondrial large ribosomal subunit; this map has a mask around the large ribosomal subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 360 pix.
= 482.4 Å		1.34 Å/pix.
x 360 pix.
= 482.4 Å		1.34 Å/pix.
x 360 pix.
= 482.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.0681 / Movie #1: 0.15
Minimum - Maximum-0.9399122 - 1.68738818
Average (Standard dev.)0.00144499 (±0.03871778)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 482.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z482.400482.400482.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-207-207-206
NX/NY/NZ414414414
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.9401.6870.001

-
Supplemental data

-
Sample components

-
Entire : Yeast Mitochondrial Large Ribosomal Subunit

EntireName: Yeast Mitochondrial Large Ribosomal Subunit
Components
  • Sample: Yeast Mitochondrial Large Ribosomal Subunit
  • Complex: Yeast Mitochondrial Large Ribosomal Subunit

-
Supramolecule #1000: Yeast Mitochondrial Large Ribosomal Subunit

SupramoleculeName: Yeast Mitochondrial Large Ribosomal Subunit / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 1.9 MDa / Theoretical: 1.9 MDa

-
Supramolecule #1: Yeast Mitochondrial Large Ribosomal Subunit

SupramoleculeName: Yeast Mitochondrial Large Ribosomal Subunit / type: complex / ID: 1 / Name.synonym: 54S Mitochondrial Ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: LSU 60S
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast / Organelle: Mitochondrion
Molecular weightExperimental: 1.9 MDa / Theoretical: 1.9 MDa

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.15 mg/mL
BufferpH: 7.5
Details: 20 mM Hepes-KOH pH 7.5, 100 mM KCl, 20 mM MgOAc, 2 mM DTT
StainingType: NEGATIVE / Details: cryo EM
GridDetails: 30 s on glow-discharged holey carbon grids (Quantifoil R2/2), onto which a home-made continuous carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK II / Method: Blot 2.5 seconds before plunging

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80 K / Max: 90 K / Average: 85 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification
DateMay 25, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 1030 / Average electron dose: 25 e/Å2
Details: An in-house built system was used to intercept the videos from the detector at a rate of 17 frames for the 1 s exposures.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION
Details: Use a newly developed statistical movie processing approach to compensate for beam-induced movement.
Number images used: 47124
FSC plot (resolution estimation)

+
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