[English] 日本語
Yorodumi
- EMDB-1780: High-resolution Cryo-EM structure of a programmed wheat germ ribosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1780
TitleHigh-resolution Cryo-EM structure of a programmed wheat germ ribosome
Map dataCryo-EM map of a programmed wheat germ ribosome containing a P-site tRNA
Sample
  • Sample: Programmed Wheat Germ 80S Ribosome
  • Complex: Tritcum aestivum 80S ribosome
KeywordsEukaryotic Ribosome / Homology Modelling / RNA Expansion Segments / Novel Ribosomal Proteins
Function / homology
Function and homology information


protein kinase activator activity / translational elongation / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / heterotrimeric G-protein complex / signaling receptor complex adaptor activity ...protein kinase activator activity / translational elongation / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / ribosome biogenesis / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / ribosome / structural constituent of ribosome / G protein-coupled receptor signaling pathway / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 ...Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L19, eukaryotic / : / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal Protein L6, KOW domain / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein L13, eukaryotic/archaeal / 60S ribosomal protein L35 / Ribosomal protein L6e / 60S ribosomal protein L6E / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L7, eukaryotic / Ribosomal_L19e / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L37ae/L37e / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / : / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / K homology domain superfamily, prokaryotic type / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature.
Similarity search - Domain/homology
60S ribosomal protein L37a, expressed / 60S ribosomal protein L21 / 40S ribosomal protein S7 / Small ribosomal subunit protein uS14 / Ribosomal protein L17 / Ribosomal protein P1 / Ribosomal protein L7 / Ribosomal protein L39 / Ribosomal protein l34 / Large ribosomal subunit protein eL30 ...60S ribosomal protein L37a, expressed / 60S ribosomal protein L21 / 40S ribosomal protein S7 / Small ribosomal subunit protein uS14 / Ribosomal protein L17 / Ribosomal protein P1 / Ribosomal protein L7 / Ribosomal protein L39 / Ribosomal protein l34 / Large ribosomal subunit protein eL30 / Ribosomal protein L18 / Ribosomal protein L13a / Ribosomal protein L11 / Ribosomal protein / 60S ribosomal protein L6 / 60S ribosomal protein L36 / Ribosomal protein L3 / S28 ribosomal protein / Ribosomal protein L19 / 30S ribosomal protein S3, chloroplastic / Large ribosomal subunit protein uL29 / Putative ribosomal protein S18 / G protein beta subunit
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 5.5 Å
AuthorsArmache JP / Jarasch A / Anger AM / Villa E / Becker T / Bhushan S / Jossinet F / Habeck M / Dindar G / Franckenberg S ...Armache JP / Jarasch A / Anger AM / Villa E / Becker T / Bhushan S / Jossinet F / Habeck M / Dindar G / Franckenberg S / Marquez V / Mielke T / Thomm M / Berninghausen O / Beatrix B / Soeding J / Westhof E / Wilson DN / Beckmann R
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
Authors: Jean-Paul Armache / Alexander Jarasch / Andreas M Anger / Elizabeth Villa / Thomas Becker / Shashi Bhushan / Fabrice Jossinet / Michael Habeck / Gülcin Dindar / Sibylle Franckenberg / Viter ...Authors: Jean-Paul Armache / Alexander Jarasch / Andreas M Anger / Elizabeth Villa / Thomas Becker / Shashi Bhushan / Fabrice Jossinet / Michael Habeck / Gülcin Dindar / Sibylle Franckenberg / Viter Marquez / Thorsten Mielke / Michael Thomm / Otto Berninghausen / Birgitta Beatrix / Johannes Söding / Eric Westhof / Daniel N Wilson / Roland Beckmann /
Abstract: Protein synthesis in all living organisms occurs on ribonucleoprotein particles, called ribosomes. Despite the universality of this process, eukaryotic ribosomes are significantly larger in size than ...Protein synthesis in all living organisms occurs on ribonucleoprotein particles, called ribosomes. Despite the universality of this process, eukaryotic ribosomes are significantly larger in size than their bacterial counterparts due in part to the presence of 80 r proteins rather than 54 in bacteria. Using cryoelectron microscopy reconstructions of a translating plant (Triticum aestivum) 80S ribosome at 5.5-Å resolution, together with a 6.1-Å map of a translating Saccharomyces cerevisiae 80S ribosome, we have localized and modeled 74/80 (92.5%) of the ribosomal proteins, encompassing 12 archaeal/eukaryote-specific small subunit proteins as well as the complete complement of the ribosomal proteins of the eukaryotic large subunit. Near-complete atomic models of the 80S ribosome provide insights into the structure, function, and evolution of the eukaryotic translational apparatus.
History
DepositionSep 6, 2010-
Header (metadata) releaseNov 26, 2010-
Map releaseDec 9, 2010-
UpdateMar 19, 2014-
Current statusMar 19, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4v7e
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1780_wg_bf03...

Downloads & links

-
Map

FileDownload / File: emd_1780.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of a programmed wheat germ ribosome containing a P-site tRNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.24 Å/pix.
x 368 pix.
= 455.4 Å		1.24 Å/pix.
x 368 pix.
= 455.4 Å		1.24 Å/pix.
x 368 pix.
= 455.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.200208 - 0.454317
Average (Standard dev.)0.00263382 (±0.0267907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-184-184-183
Dimensions368368368
Spacing368368368
CellA=B=C: 455.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.23751.23751.2375
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z455.400455.400455.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S213
start NC/NR/NS-184-184-183
NC/NR/NS368368368
D min/max/mean-0.2000.4540.003

-
Supplemental data

-
Sample components

-
Entire : Programmed Wheat Germ 80S Ribosome

EntireName: Programmed Wheat Germ 80S Ribosome
Components
  • Sample: Programmed Wheat Germ 80S Ribosome
  • Complex: Tritcum aestivum 80S ribosome

-
Supramolecule #1000: Programmed Wheat Germ 80S Ribosome

SupramoleculeName: Programmed Wheat Germ 80S Ribosome / type: sample / ID: 1000 / Oligomeric state: One Ribosome / Number unique components: 1
Molecular weightExperimental: 4.2 MDa / Theoretical: 4.2 MDa / Method: Sedimentation

-
Supramolecule #1: Tritcum aestivum 80S ribosome

SupramoleculeName: Tritcum aestivum 80S ribosome / type: complex / ID: 1 / Name.synonym: Wheat Germ Ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Triticum aestivum (bread wheat) / synonym: Bread wheat
Molecular weightExperimental: 4.2 MDa / Theoretical: 4.2 MDa

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES/KOH, pH 7.5, 100 mM KOAc, 10 mM Mg(OAc)2, 0.01 mg/ml cycloheximide, 1 mM DTT, 0.01 % Nikkol
StainingType: NEGATIVE / Details: Cryo-EM
GridDetails: Quantifoil Grid with 2 nm carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot
Method: Blot for 10 seconds before plunging, use 2 layers of filter paper

-
Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 4.76 µm / Number real images: 1374 / Average electron dose: 25 e/Å2
Details: Scanned at 5334 dpi on a Heidelberg Primescan Drum Scanner
Od range: 1.2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 39000
Sample stageSpecimen holder: FEI Polara Cartridge System / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

DetailsThe reconstruction contains 2108230 particles in total
CTF correctionDetails: Wiener Filter on 3D volumes (SPIDER)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER

+
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