[English] 日本語
Yorodumi
- PDB-1zn1: Coordinates of RRF fitted into Cryo-EM map of the 70S post-termin... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1zn1
TitleCoordinates of RRF fitted into Cryo-EM map of the 70S post-termination complex
Components
  • 30S ribosomal protein S12
  • Ribosome recycling factor
  • ribosomal 16S RNA
  • ribosomal 23S RNA
KeywordsBIOSYNTHETIC/structural protein/RNA / ribosome recycling factor / elongation factor G / 70S / post-termination complex / BIOSYNTHETIC-structural protein-RNA COMPLEX
Function / homologyRRF superfamily / Ribosome recycling factor domain / Ribosomal protein S12 signature. / Ribosome recycling factor / Nucleic acid-binding, OB-fold / Ribosomal protein S12/S23 / Ribosomal protein S12, bacterial-type / Ribosome recycling factor / Ribosomal protein S12/S23 / cytoplasmic translational termination ...RRF superfamily / Ribosome recycling factor domain / Ribosomal protein S12 signature. / Ribosome recycling factor / Nucleic acid-binding, OB-fold / Ribosomal protein S12/S23 / Ribosomal protein S12, bacterial-type / Ribosome recycling factor / Ribosomal protein S12/S23 / cytoplasmic translational termination / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / cytosol / cytoplasm / 30S ribosomal protein S12 / Ribosome-recycling factor
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 14.1 Å resolution
AuthorsGao, N. / Zavialov, A.V. / Li, W. / Sengupta, J. / Valle, M. / Gursky, R.P. / Ehrenberg, M. / Frank, J.
Citation
Journal: Mol. Cell / Year: 2005
Title: Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
Authors: Ning Gao / Andrey V Zavialov / Wen Li / Jayati Sengupta / Mikel Valle / Richard P Gursky / Måns Ehrenberg / Joachim Frank
#1: Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: Locking and unlocking of ribosomal motions
Authors: Valle, M. / Zavialov, A. / Sengupta, J. / Rawat, U. / Ehrenberg, M. / Frank, J.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: Study of structural dynamics of E.coli 70S ribosome using real-space refinement
Authors: Gao, H. / Sengupta, J. / Valle, M. / Korostelev, A. / Eswar, N. / Stagg, S.M. / Van Roey, P. / Agrawal, R.K. / Harvey, S.C. / Sali, A. / Chapman, M.S. / Frank, J.
#3: Journal: Embo J. / Year: 2000
Title: Crystal structure of the ribosome recycling factor from E.coli
Authors: Kim, K.K. / Min, K. / Suh, S.W.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 11, 2005 / Release: Jun 14, 2005
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 14, 2005Structure modelrepositoryInitial release
1.1Apr 30, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jan 31, 2018Structure modelData collection / Database referencescitation_author / em_image_scans_citation_author.name
Remark 999SEQUENCE This entry contains C alpha and P atoms only.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1127
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1128
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1128
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: ribosomal 23S RNA
C: ribosomal 16S RNA
A: Ribosome recycling factor
L: 30S ribosomal protein S12


Theoretical massNumber of molelcules
Total (without water)63,4414
Polyers63,4414
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: RNA chain ribosomal 23S RNA / Coordinate model: P atoms only


Mass: 18952.248 Da / Num. of mol.: 1 / Fragment: fragment of large subunit rRNA helix 69-71 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia
#2: RNA chain ribosomal 16S RNA / Coordinate model: P atoms only


Mass: 12988.728 Da / Num. of mol.: 1 / Fragment: fragment of small subunit rRNA helix 44 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia
#3: Protein/peptide Ribosome recycling factor / / Ribosome releasing factor / RRF / Coordinate model: Cα atoms only


Mass: 20671.621 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A805
#4: Protein/peptide 30S ribosomal protein S12 / / Coordinate model: Cα atoms only


Mass: 10828.608 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / References: UniProt: P0A7S3

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 70S ribosomeRibosome / Type: RIBOSOME
Buffer solutionName: Polymix buffer / Details: Polymix buffer / pH: 7.5
SpecimenConc.: 0.032 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holey 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
MicroscopyMicroscope model: FEI TECNAI F20 / Date: Feb 1, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 / Calibrated magnification: 49700 / Nominal defocus max: -3.8 nm / Nominal defocus min: -1.4 nm
Specimen holderTemperature: 93 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

-
Processing

CTF correctionDetails: CTF correction of 3D maps by Wiener filtration
SymmetryPoint symmetry: C1
3D reconstructionMethod: 3D projection matching; conjugate gradient with regularization
Resolution: 14.1 Å / Number of particles: 37379 / Actual pixel size: 2.82 / Magnification calibration: TMV / Details: SPIDER package / Symmetry type: POINT
Atomic model buildingDetails: METHOD--Manual fitting in O / Ref protocol: OTHER / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
11P6G1
21P851
31EK81
Number of atoms included #LASTProtein: 282 / Nucleic acid: 99 / Ligand: 0 / Solvent: 0 / Total: 381

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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