[English] 日本語
Yorodumi
- PDB-3iyx: Coordinates of the b1b bridge-forming protein structures fitted i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iyx
TitleCoordinates of the b1b bridge-forming protein structures fitted into the Cryo-EM map of E.coli 70S ribosome (EMD-1056)
Components
  • 30S ribosomal protein S13
  • 50S ribosomal protein L31
  • 50S ribosomal protein L5
KeywordsRIBOSOMAL PROTEIN / Ribosomal intersubunit bridges / B1b-bridge / Ratchet-like motion / Ribosomal protein L31
Function / homology
Function and homology information


tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L5, bacterial-type / Ribosomal protein S13, bacterial-type / L28p-like / Ribosomal protein L5, conserved site / Ribosomal protein L5, N-terminal ...Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L5, bacterial-type / Ribosomal protein S13, bacterial-type / L28p-like / Ribosomal protein L5, conserved site / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein S13, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein L5 / ribosomal L5P family C-terminus / Ribosomal protein S13/S18 / Ribosomal protein S13-like, H2TH / Ribosomal protein S13 signature. / Ribosomal protein S13 family profile.
Similarity search - Domain/homology
30S ribosomal protein S13 / 50S ribosomal protein L5 / 50S ribosomal protein L31
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsShasmal, M. / Chakraborty, B. / Sengupta, J.
CitationJournal: Biochem Biophys Res Commun / Year: 2010
Title: Intrinsic molecular properties of the protein-protein bridge facilitate ratchet-like motion of the ribosome.
Authors: Manidip Shasmal / Biprashekhar Chakraborty / Jayati Sengupta /
Abstract: The ribosomal intersubunit bridges maintain the overall architecture of the ribosome and thereby play a pivotal role in the dynamics of translation. The only protein-protein bridge, b1b, is formed by ...The ribosomal intersubunit bridges maintain the overall architecture of the ribosome and thereby play a pivotal role in the dynamics of translation. The only protein-protein bridge, b1b, is formed by the two proteins, S13 and L5 of the small and large ribosomal subunits, respectively. B1b absorbs the largest movement during ratchet-like motion, and its two proteins reorganize in different constellations during this motion of the ribosome. Our results in this study of b1b in the Escherichia coli 70S ribosome suggest that the intrinsic molecular features of the bridging proteins allow the bridge to modulate the ratchet-like motion in a controlled manner. Additionally, another large subunit protein, L31, seems to participate with S13 and L5 in the formation, dynamics, and stabilization of this bridge.
History
DepositionJul 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4Feb 21, 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 / 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1056
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1056
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
M: 30S ribosomal protein S13
F: 50S ribosomal protein L5
A: 50S ribosomal protein L31


Theoretical massNumber of molelcules
Total (without water)41,3493
Polymers41,3493
Non-polymers00
Water0
1


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

-
Components

#1: Protein 30S ribosomal protein S13 / / Coordinate model: Cα atoms only


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: O55:H7 / References: UniProt: D3QTD7
#2: Protein 50S ribosomal protein L5 / / Coordinate model: Cα atoms only


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: O55:H7 / References: UniProt: D3QTE7
#3: Protein 50S ribosomal protein L31 / / Coordinate model: Cα atoms only


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: O55:H7 / References: UniProt: D3QYD6

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: E.coli 70S ribosome / Type: RIBOSOME
Buffer solutionName: Polymix buffer / pH: 7.5 / Details: Polymix buffer
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holley carbon film grids
VitrificationCryogen name: ETHANE / Details: Rapid-freezing in liquid ethane

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 49696 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 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

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: CTF correction of 3D maps by Wiener filteration
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Single ParticleSingle particle analysis / Resolution: 9 Å / Num. of particles: 52181 / Nominal pixel size: 2.82 Å / Magnification calibration: TMV / Symmetry type: POINT
Atomic model building
ID
1
2
3
Atomic model building

Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-ID 3D fitting-IDAccession codeInitial refinement model-IDDetails
12I2P

2i2p
PDB Unreleased entry

M12I2P1
22I2T

2i2t
PDB Unreleased entry

F22I2T2
32WRJ

2wrj
PDB Unreleased entry

432WRJ32WRJ CHAIN 4 (TEMPLATE FOR HOMOLOGY MODELLING)
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms362 0 0 0 362

+
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