[English] 日本語
Yorodumi
- EMDB-5116: 30S subunit of ribosomal protein S1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5116
Title30S subunit of ribosomal protein S1
Map datasurface view of S1 protein
Sample
  • Sample: Protein S1
  • Protein or peptide: Protein S1
Keywordsprotein S1 / EM density / spider / ribosome / single particle reconstruction
Biological speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsSengupta J / Agrawal RK / Frank J
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2001
Title: Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA.
Authors: J Sengupta / R K Agrawal / J Frank /
Abstract: S1 is the largest ribosomal protein, present in the small subunit of the bacterial ribosome. It has a pivotal role in stabilizing the mRNA on the ribosome. Thus far, S1 has eluded structural ...S1 is the largest ribosomal protein, present in the small subunit of the bacterial ribosome. It has a pivotal role in stabilizing the mRNA on the ribosome. Thus far, S1 has eluded structural determination. We have identified the S1 protein mass in the cryo-electron microscopic map of the Escherichia coli ribosome by comparing the map with a recent x-ray crystallographic structure of the 30S subunit, which lacks S1. According to our finding, S1 is located at the junction of head, platform, and main body of the 30S subunit, thus explaining all existing biochemical and crosslinking data. Protein S1 as identified in our map has a complex, elongated shape with two holes in its central portion. The N-terminal domain, forming one of the extensions, penetrates into the head of the 30S subunit. Evidence for direct interaction of S1 with 11 nucleotides of the mRNA, immediately upstream of the Shine-Dalgarno sequence, explains the protein's role in the recognition of the 5' region of mRNA.
#1: Journal: CELL (CAMBRIDGE,MASS.) / Year: 2000
Title: Solution structure of the E. coli 70S ribosome at 11.5 angstrom resolution
Authors: Gabashvili IS / Agrawal RK / Spahn CMT / Grassucci RA / Svergun DI / Frank J / Penczek P
History
DepositionApr 13, 2009-
Header (metadata) releaseApr 20, 2009-
Map releaseApr 20, 2009-
UpdateJul 7, 2010-
Current statusJul 7, 2010Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 30
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 30
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5116_1.png

Downloads & links

-
Map

FileDownload / File: emd_5116.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsurface view of S1 protein
Voxel sizeX=Y=Z: 2.93 Å
Density
Contour Level1: 20.0 / Movie #1: 30
Minimum - Maximum-19.281300000000002 - 183.097000000000008
Average (Standard dev.)0.108505 (±2.95157)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions125125125
Spacing125125125
CellA=B=C: 366.25 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.932.932.93
M x/y/z125125125
origin x/y/z0.0000.0000.000
length x/y/z366.250366.250366.250
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS125125125
D min/max/mean-19.281183.0970.109

-
Supplemental data

-
Sample components

-
Entire : Protein S1

EntireName: Protein S1
Components
  • Sample: Protein S1
  • Protein or peptide: Protein S1

-
Supramolecule #1000: Protein S1

SupramoleculeName: Protein S1 / type: sample / ID: 1000
Details: see additional reference by Gabashvili I S, Agrawal R K, Spahn C M T, Grassucci R,Svergun D I,and Frank J, 7. Penczek P (2000) Cell 100,537-549
Number unique components: 1

-
Macromolecule #1: Protein S1

MacromoleculeName: Protein S1 / type: protein_or_peptide / ID: 1 / Name.synonym: Protein S1 / Number of copies: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI 20
DateJul 1, 1999
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder.
Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

CTF correctionDetails: see the additional reference
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: OTHER / Software - Name: spider / Details: see the additional reference

+
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://pdbjlvh1.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