[English] 日本語
Yorodumi
- EMDB-1363: Locking and unlocking of ribosomal motions. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1363
TitleLocking and unlocking of ribosomal motions.
Map dataCryo-EM map of E.coli 70S ribosome
Sample
  • Sample: EF-G bound Release Complex in the presence of Puromycin and GDPNP
  • Complex: Release Complex
  • Ligand: Puromycin
  • Ligand: EF-G
  • Ligand: GDPNP
Function / homology
Function and homology information


translational elongation / translation elongation factor activity / GDP binding / ribosome binding / small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome ...translational elongation / translation elongation factor activity / GDP binding / ribosome binding / small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / GTP binding / magnesium ion binding / metal ion binding / cytoplasm
Similarity search - Function
Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus ...Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L5, bacterial-type / Ribosomal protein S13, bacterial-type / L28p-like / Ribosomal protein S12, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / 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. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S13-like, H2TH / Small GTP-binding protein domain / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
30S ribosomal protein S13 / 50S ribosomal protein L5 / 50S ribosomal protein L31 / Elongation factor G / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS12
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.9 Å
AuthorsMikel V / Andrey Z / Sengupta J / Rawat U / Ehrenberg M / Frank J
CitationJournal: Cell / Year: 2003
Title: Locking and unlocking of ribosomal motions.
Authors: Mikel Valle / Andrey Zavialov / Jayati Sengupta / Urmila Rawat / Måns Ehrenberg / Joachim Frank /
Abstract: During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the ...During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the direction of the mRNA movement. By means of cryo-electron microscopy we observe that this rotation is accompanied by a 20 A movement of the L1 stalk of the 50S subunit, implying that this region is involved in the translocation of deacylated tRNAs from the P to the E site. These ribosomal motions can occur only when the P-site tRNA is deacylated. Prior to peptidyl-transfer to the A-site tRNA or peptide removal, the presence of the charged P-site tRNA locks the ribosome and prohibits both of these motions.
History
DepositionMay 21, 2007-
Header (metadata) releaseMay 24, 2007-
Map releaseMay 24, 2007-
UpdateNov 7, 2012-
Current statusNov 7, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-1pn6, PDB-1pn7, PDB-1pn8
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3iyy
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1pn6
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1pn7
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1pn8
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2z9q
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iyy
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3izp
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1363.gif

Downloads & links

-
Map

FileDownload / File: emd_1363.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of E.coli 70S ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.82 Å/pix.
x 130 pix.
= 366.6 Å		2.82 Å/pix.
x 130 pix.
= 366.6 Å		2.82 Å/pix.
x 130 pix.
= 366.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.82 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 56.799999999999997 / Movie #1: 50
Minimum - Maximum-116.941999999999993 - 253.153999999999996
Average (Standard dev.)2.69052 (±25.7986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-65-65-65
Dimensions130130130
Spacing130130130
CellA=B=C: 366.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.822.822.82
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z366.600366.600366.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-116.942253.1542.691

-
Supplemental data

-
Sample components

-
Entire : EF-G bound Release Complex in the presence of Puromycin and GDPNP

EntireName: EF-G bound Release Complex in the presence of Puromycin and GDPNP
Components
  • Sample: EF-G bound Release Complex in the presence of Puromycin and GDPNP
  • Complex: Release Complex
  • Ligand: Puromycin
  • Ligand: EF-G
  • Ligand: GDPNP

-
Supramolecule #1000: EF-G bound Release Complex in the presence of Puromycin and GDPNP

SupramoleculeName: EF-G bound Release Complex in the presence of Puromycin and GDPNP
type: sample / ID: 1000 / Number unique components: 4

-
Supramolecule #1: Release Complex

SupramoleculeName: Release Complex / type: complex / ID: 1 / Details: mRNA and tRNA / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600

-
Macromolecule #1: Puromycin

MacromoleculeName: Puromycin / type: ligand / ID: 1 / Details: Antibiotic / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)
Chemical component information

ChemComp-PUY:
PUROMYCIN / antibiotic, inhibitor*YM

-
Macromolecule #2: EF-G

MacromoleculeName: EF-G / type: ligand / ID: 2 / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600

-
Macromolecule #3: GDPNP

MacromoleculeName: GDPNP / type: ligand / ID: 3 / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER / Details: Rapid-freezing in liquid ethane

-
Electron microscopy

MicroscopeFEI TECNAI 20
TemperatureAverage: 93 K
Alignment procedureLegacy - Electron beam tilt params: 0
DateJul 11, 2003
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49696 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder: cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

CTF correctionDetails: CTF correctionn of 3D map
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, package / Number images used: 1

+
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