[English] 日本語
Yorodumi
- PDB-1zc8: Coordinates of tmRNA, SmpB, EF-Tu and h44 fitted into Cryo-EM map... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zc8
TitleCoordinates of tmRNA, SmpB, EF-Tu and h44 fitted into Cryo-EM map of the 70S ribosome and tmRNA complex
Components
  • (protein kinase ...) x 4
  • Elongation factor TuEF-Tu
  • H2 16S rRNA
  • H2b d mRNA
  • H44 16S ribosomal RNA
  • H5 16S ribosomal RNA
  • SsrA-binding protein
  • TLD 16S ribosomal RNA
KeywordsRNA binding protein/RNA / SmpB / tmRNA / EF-Tu / h44 / 30S / 16s rRNA / Cryo-EM / trans-translation / 70S / RNA binding protein-RNA COMPLEX
Function / homology
Function and homology information


trans-translation / translation elongation factor activity / GTPase activity / GTP binding / RNA binding / cytosol / cytoplasm
Similarity search - Function
SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain ...SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / SsrA-binding protein / Elongation factor Tu-A
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13 Å
AuthorsValle, M. / Gillet, R. / Kaur, S. / Henne, A. / Ramakrishnan, V. / Frank, J.
Citation
Journal: Science / Year: 2003
Title: Visualizing tmRNA entry into a stalled ribosome.
Authors: Mikel Valle / Reynald Gillet / Sukhjit Kaur / Anke Henne / V Ramakrishnan / Joachim Frank /
Abstract: Bacterial ribosomes stalled on defective messenger RNAs (mRNAs) are rescued by tmRNA, an approximately 300-nucleotide-long molecule that functions as both transfer RNA (tRNA) and mRNA. Translation ...Bacterial ribosomes stalled on defective messenger RNAs (mRNAs) are rescued by tmRNA, an approximately 300-nucleotide-long molecule that functions as both transfer RNA (tRNA) and mRNA. Translation then switches from the defective message to a short open reading frame on tmRNA that tags the defective nascent peptide chain for degradation. However, the mechanism by which tmRNA can enter and move through the ribosome is unknown. We present a cryo-electron microscopy study at approximately 13 to 15 angstroms of the entry of tmRNA into the ribosome. The structure reveals how tmRNA could move through the ribosome despite its complicated topology and also suggests roles for proteins S1 and SmpB in the function of tmRNA.
#1: Journal: Embo J. / Year: 2002
Title: Structure of small protein B: the protein component of the tmRNA SmpB system for ribosome rescue
Authors: Dong, G. / Nowakowski, J. / Hoffman, D.W.
#3: Journal: Embo J. / Year: 2002
Title: Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process
Authors: Valle, M. / Sengupta, J. / Swami, N.K. / Grassucci, R.A. / Burkhardt, N. / Nierhaus, K.H. / Agrawal, R.K. / Frank, J.
#4: Journal: Structure Fold.Des. / Year: 1999
Title: E. Coli Cysteinyl-tRNA and T. Aquaticus Elongation Factor Ef-Tu: GTP Ternary Complex
Authors: Nissen, P. / Kjeldgaard, M. / Thirup, S. / Nyborg, J.
#5: Journal: Cell(Cambridge,Mass.) / Year: 2002
Title: Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form
Authors: Ogle, J.M. / Murphy Iv, F.V. / Tarry, M.J. / Ramakrishnan, V.
History
DepositionApr 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2013Group: Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_image_scans / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type
Remark 999SEQUENCE Author states that the map was for Thermus thermophilus, but the EF-Tu model was from ...SEQUENCE Author states that the map was for Thermus thermophilus, but the EF-Tu model was from Thermus aquaticus (SWS code Q01698).

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1122
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1122
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TLD 16S ribosomal RNA
B: H2 16S rRNA
C: H2b d mRNA
G: protein kinase 4 mRNA
F: H5 16S ribosomal RNA
H: protein kinase 2 mRNA
I: protein kinase 3
J: protein kinase 4 mRNA
Z: H44 16S ribosomal RNA
K: SsrA-binding protein
Y: Elongation factor Tu


Theoretical massNumber of molelcules
Total (without water)194,00211
Polymers194,00211
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
RNA chain , 5 types, 5 molecules ABCFZ

#1: RNA chain TLD 16S ribosomal RNA / Coordinate model: P atoms only


Mass: 18951.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#2: RNA chain H2 16S rRNA / Coordinate model: P atoms only


Mass: 5162.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#3: RNA chain H2b d mRNA / Coordinate model: P atoms only


Mass: 10013.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#5: RNA chain H5 16S ribosomal RNA / Coordinate model: P atoms only


Mass: 9206.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#9: RNA chain H44 16S ribosomal RNA / Coordinate model: P atoms only


Mass: 29593.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)

-
Protein kinase ... , 4 types, 4 molecules GHIJ

#4: RNA chain protein kinase 4 mRNA / Coordinate model: P atoms only


Mass: 9738.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pk1 / Source: (natural) Thermus thermophilus (bacteria)
#6: RNA chain protein kinase 2 mRNA / Coordinate model: P atoms only


Mass: 18915.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pk2 / Source: (natural) Thermus thermophilus (bacteria)
#7: RNA chain protein kinase 3 / / Coordinate model: P atoms only


Mass: 15808.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pk3 / Source: (natural) Thermus thermophilus (bacteria)
#8: RNA chain protein kinase 4 mRNA / Coordinate model: P atoms only


Mass: 16781.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pk4 / Source: (natural) Thermus thermophilus (bacteria)

-
Protein , 2 types, 2 molecules KY

#10: Protein SsrA-binding protein / Coordinate model: Cα atoms only


Mass: 15087.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: O66640*PLUS
#11: Protein Elongation factor Tu / EF-Tu / EF-Tu / Coordinate model: Cα atoms only


Mass: 44742.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN6*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: 70S ribosomeRibosome / Type: RIBOSOME
Buffer solutionpH: 7.5
SpecimenConc.: 0.032 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holley-carbon film grids
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Aug 1, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 49000 X / Calibrated magnification: 52000 X / Nominal defocus max: 1450 nm / Nominal defocus min: 3700 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

CTF correctionDetails: CTF correction of 3D-maps by Wiener filtration
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 3D projection matching: conjugate gradients with regularization
Resolution: 13 Å / Num. of particles: 27644 / Actual pixel size: 2.82 Å / Magnification calibration: TMV
Details: SPIDER package, This entry contains only C alpha and P atoms.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--manual fitting in O
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11K8H11K8H1PDBexperimental model
21B2311B232PDBexperimental model
31N3211N323PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms535 416 0 0 951

+
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