[English] 日本語
Yorodumi
- EMDB-1524: Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1524
TitleComplex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP
Map dataComplex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP
Sample
  • Sample: Complex of elongating Escherichia coli 70S ribosome (2tRNAs) and EF4(LepA)-GMPPNP
  • Complex: 70S ribosomeRibosome
  • Protein or peptide: EF4(LepA)
  • RNA: A-tRNA
  • RNA: P-tRNA
Keywordsribosome / translation / LepA / EF4
Function / homology
Function and homology information


: / response to pH / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / misfolded RNA binding / ribosomal small subunit binding / Group I intron splicing / RNA folding / translational termination ...: / response to pH / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / misfolded RNA binding / ribosomal small subunit binding / Group I intron splicing / RNA folding / translational termination / response to salt stress / translation elongation factor activity / response to cold / positive regulation of RNA splicing / positive regulation of translation / maintenance of translational fidelity / ribosomal small subunit biogenesis / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / GTP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Elongation factor 4 / GTP-binding protein LepA, C-terminal / Elongation factor 4, domain IV / LepA, C-terminal domain superfamily / GTP-binding protein LepA 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. ...Elongation factor 4 / GTP-binding protein LepA, C-terminal / Elongation factor 4, domain IV / LepA, C-terminal domain superfamily / GTP-binding protein LepA 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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 S12, bacterial-type / Small GTP-binding protein domain / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS12 / Elongation factor 4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.9 Å
AuthorsConnell SR / Topf M / Qin Y / Wilson DN / Mielke T / Fucini P / Nierhaus KH / Spahn CMT
CitationJournal: Nat Struct Mol Biol / Year: 2008
Title: A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation.
Authors: Sean R Connell / Maya Topf / Yan Qin / Daniel N Wilson / Thorsten Mielke / Paola Fucini / Knud H Nierhaus / Christian M T Spahn /
Abstract: EF4 (LepA) is an almost universally conserved translational GTPase in eubacteria. It seems to be essential under environmental stress conditions and has previously been shown to back-translocate the ...EF4 (LepA) is an almost universally conserved translational GTPase in eubacteria. It seems to be essential under environmental stress conditions and has previously been shown to back-translocate the tRNAs on the ribosome, thereby reverting the canonical translocation reaction. In the current work, EF4 was directly visualized in the process of back-translocating tRNAs by single-particle cryo-EM. Using flexible fitting methods, we built a model of ribosome-bound EF4 based on the cryo-EM map and a recently published unbound EF4 X-ray structure. The cryo-EM map establishes EF4 as a noncanonical elongation factor that interacts not only with the elongating ribosome, but also with the back-translocated tRNA in the A-site region, which is present in a previously unseen, intermediate state and deviates markedly from the position of a canonical A-tRNA. Our results, therefore, provide insight into the underlying structural principles governing back-translocation.
History
DepositionJun 10, 2008-
Header (metadata) releaseJun 10, 2008-
Map releaseApr 1, 2009-
UpdateApr 16, 2014-
Current statusApr 16, 2014Processing site: PDBe / Status: Released

-
Structure visualization

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

Downloads & links

-
Map

FileDownload / File: emd_1524.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComplex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
2.52 Å/pix.
x 150 pix.
= 378. Å
2.52 Å/pix.
x 150 pix.
= 378. Å
2.52 Å/pix.
x 150 pix.
= 378. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.52 Å
Density
Contour Level1: 1.0 / Movie #1: 1
Minimum - Maximum-5.05751 - 11.5594
Average (Standard dev.)0.00000000080912 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-75-75-74
Dimensions150150150
Spacing150150150
CellA=B=C: 378 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.522.522.52
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z378.000378.000378.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-75-75-74
NX/NY/NZ150150150
MAP C/R/S213
start NC/NR/NS-75-75-74
NC/NR/NS150150150
D min/max/mean-5.05811.5590.000

-
Supplemental data

-
Sample components

-
Entire : Complex of elongating Escherichia coli 70S ribosome (2tRNAs) and ...

EntireName: Complex of elongating Escherichia coli 70S ribosome (2tRNAs) and EF4(LepA)-GMPPNP
Components
  • Sample: Complex of elongating Escherichia coli 70S ribosome (2tRNAs) and EF4(LepA)-GMPPNP
  • Complex: 70S ribosomeRibosome
  • Protein or peptide: EF4(LepA)
  • RNA: A-tRNA
  • RNA: P-tRNA

-
Supramolecule #1000: Complex of elongating Escherichia coli 70S ribosome (2tRNAs) and ...

SupramoleculeName: Complex of elongating Escherichia coli 70S ribosome (2tRNAs) and EF4(LepA)-GMPPNP
type: sample / ID: 1000 / Number unique components: 4
Molecular weightTheoretical: 2.6 MDa

-
Supramolecule #1: 70S ribosome

SupramoleculeName: 70S ribosome / type: complex / ID: 1 / Name.synonym: 70S ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: EF4(LepA)

MacromoleculeName: EF4(LepA) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET14b

-
Macromolecule #2: A-tRNA

MacromoleculeName: A-tRNA / type: rna / ID: 2 / Name.synonym: A-tRNA / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #3: P-tRNA

MacromoleculeName: P-tRNA / type: rna / ID: 3 / Name.synonym: P-tRNA / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferDetails: 20 mM HEPES-KOH (pH 7.6), 4.5 mM Mg(CH3COO)2, 150 mM NH4CH3COO, 4 mM B-mercaptoethanol, 2 mM spermidine, and 0.05 mM spermine
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: OTHER / Details: Vitrification instrument: vitrobot

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 39000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 4.7 µm / Average electron dose: 20 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Defocus groups
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider / Number images used: 41294

-
Atomic model buiding 1

Initial modelPDB ID:

2i2p
PDB Unreleased entry

SoftwareName: SITUS
DetailsProtocol: Rigid Body. the subunit was fitted using situs
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-3deg:
Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP

-
Atomic model buiding 2

Initial modelPDB ID:

2i2t
PDB Unreleased entry

SoftwareName: SITUS
DetailsProtocol: Rigid Body. the subunit was fitted using situs
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-3deg:
Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP

-
Atomic model buiding 3

Initial modelPDB ID:
SoftwareName: Mod-EM and Flex-EM
DetailsProtocol: Rigid Body and flexible fitting. the protein was first rigidly fit with Mod-EM and then flexibly fit with Flex-EM
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation
Output model

PDB-3deg:
Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP

+
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