[English] 日本語
Yorodumi
- EMDB-4319: uL23 beta hairpin loop deletion of E.coli ribosome -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 4319
TitleuL23 beta hairpin loop deletion of E.coli ribosome
Map dataSharpened map of E.coli ribosome with the beta-hairpin of uL23 deleted.
SampleE.coli ribosome with beta-hairpin of uL23 deleted:
50S ribosomal protein L23
Function / homologyRibosomal protein L23/L25, conserved site / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L25/L23 / Ribosomal protein L23 / Ribosomal protein L23 signature. / ribosome / rRNA binding / structural constituent of ribosome / translation / 50S ribosomal protein L23
Function and homology information
SourceEscherichia coli (E. coli) / Escherichia coli O157:H7 (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsKudva R / von Heijne G / Carroni M
CitationJournal: Elife / Year: 2018
Title: The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding.
Authors: Renuka Kudva / Pengfei Tian / Fátima Pardo-Avila / Marta Carroni / Robert B Best / Harris D Bernstein / Gunnar von Heijne
Validation ReportPDB-ID: 6fu8

SummaryFull reportAbout validation report
DateDeposition: Feb 26, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Dec 5, 2018 / Last update: Dec 26, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.536
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.536
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6fu8
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6fu8
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_4319.map.gz (map file in CCP4 format, 389345 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
460 pix
1.09 Å/pix.
= 501.4 Å
460 pix
1.09 Å/pix.
= 501.4 Å
460 pix
1.09 Å/pix.
= 501.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density
Contour Level:0.536 (by author), 0.536 (movie #1):
Minimum - Maximum-0.5661596 - 1.9835955
Average (Standard dev.)-0.009908884 (0.12531587)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions460460460
Origin0.00.00.0
Limit459.0459.0459.0
Spacing460460460
CellA=B=C: 501.40002 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z501.400501.400501.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS460460460
D min/max/mean-0.5661.984-0.010

-
Supplemental data

-
Mask #1

Fileemd_4319_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

-
Sample components

-
Entire E.coli ribosome with beta-hairpin of uL23 deleted

EntireName: E.coli ribosome with beta-hairpin of uL23 deleted
Details: Deposited PDB is of the uL23 with the beta-hairpin loop deleted.
Number of components: 2

-
Component #1: protein, E.coli ribosome with beta-hairpin of uL23 deleted

ProteinName: E.coli ribosome with beta-hairpin of uL23 deleted
Details: Deposited PDB is of the uL23 with the beta-hairpin loop deleted.
Recombinant expression: No
MassTheoretical: 2.6 MDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Component #2: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.324003 kDa
SourceSpecies: Escherichia coli O157:H7 (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.17 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 3500

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 132029
3D reconstructionAlgorithm: BACK PROJECTION / Software: cryoSPARC / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
Details: All processing from ab initio to refinement and sharpening performed in cryosparc
FSC plot
(resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. 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

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