[English] 日本語
Yorodumi
- EMDB-2604: Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES in a ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 2604
TitleKluyveromyces lactis 80S ribosome in complex with CrPV-IRES in a rotated stated with masked 40S
Map dataMap generated through masking the 40S subunit from the EMD-12385 map and performing a re-classification followed by re-refinement both process in the presence of the mask.
SampleKluyveromyces lactis 80S ribosome in complex with CrPV-IRES with 40S masked and re-refined:
ribosome-eukaryote / CrPV-IRES
Keywordstranslation / ribosomes / eukaryote / initiation
SourceKluyveromyces lactis (Kluyveromyces lactis) / Cricket paralysis virus
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsFernandez IS / Bai X / Scheres SHW / Ramakrishnan V
CitationJournal: Cell / Year: 2014
Title: Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome.
Authors: Israel S Fernández / Xiao-Chen Bai / Garib Murshudov / Sjors H W Scheres / V Ramakrishnan
Abstract: The cricket paralysis virus internal ribosome entry site (CrPV-IRES) is a folded structure in a viral mRNA that allows initiation of translation in the absence of any host initiation factors. By ...The cricket paralysis virus internal ribosome entry site (CrPV-IRES) is a folded structure in a viral mRNA that allows initiation of translation in the absence of any host initiation factors. By using recent advances in single-particle electron cryomicroscopy, we have solved the structure of CrPV-IRES bound to the ribosome of the yeast Kluyveromyces lactis in both the canonical and rotated states at overall resolutions of 3.7 and 3.8 Å, respectively. In both states, the pseudoknot PKI of the CrPV-IRES mimics a tRNA/mRNA interaction in the decoding center of the A site of the 40S ribosomal subunit. The structure and accompanying factor-binding data show that CrPV-IRES binding mimics a pretranslocation rather than initiation state of the ribosome. Translocation of the IRES by elongation factor 2 (eEF2) is required to bring the first codon of the mRNA into the A site and to allow the start of translation.
Validation ReportPDB-ID: 4v92

SummaryFull reportAbout validation report
DateDeposition: Mar 5, 2014 / Header (metadata) release: Apr 9, 2014 / Map release: May 21, 2014 / Last update: Jun 11, 2014

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-4v92
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-4v92
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_2604.map.gz (map file in CCP4 format, 128001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.34 Å/pix.
= 428.8 Å
320 pix
1.34 Å/pix.
= 428.8 Å
320 pix
1.34 Å/pix.
= 428.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour Level:0.07 (by author), 0.07 (movie #1):
Minimum - Maximum-0.61792678 - 0.99048573
Average (Standard dev.)0.00144863 (0.02323123)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 428.80002 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z428.800428.800428.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.6180.9900.001

-
Supplemental data

-
Sample components

-
Entire Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES with ...

EntireName: Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES with 40S masked and re-refined
Number of components: 2

-
Component #1: ribosome-eukaryote, Kluyveromyces lactis 40S ribosome

Ribosome-eukaryoteName: Kluyveromyces lactis 40S ribosome / Eukaryote: SSU 40S, SSU RNA 18S / Recombinant expression: No
SourceSpecies: Kluyveromyces lactis (Kluyveromyces lactis)

-
Component #2: protein, CrPV-IRES

ProteinName: CrPV-IRES / Recombinant expression: No
SourceSpecies: Cricket paralysis virus

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/ml
Buffer solution: MES-KOH, 40mM K-acetate, 10mM NH4-acetate, 8mM Mg-acetate, 2mM DTT
pH: 6.5
Support film400mesh Cu, Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: PROPANE / Temperature: 120 K / Humidity: 90 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Jul 7, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: OTHER
LensMagnification: 47000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1.8 - 3 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 1900

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 25969
Details: Masked 40S area and focused classification and refined in the presence of the mask
3D reconstructionAlgorithm: Relion / Software: Relion / CTF correction: Each particle / Resolution: 3.8 Å / Resolution method: FSC 0.143, gold-standard

-
Atomic model buiding

Modeling #1Software: Chimera, refmac / Refinement protocol: flexible / Target criteria: R-factor, FSC / Refinement space: RECIPROCAL
Input PDB model: 3U5B
Overall bvalue: 60
Modeling #2Software: Chimera, refmac / Refinement protocol: flexible / Target criteria: R-factor, FSC / Refinement space: RECIPROCAL
Input PDB model: 3U5C
Overall bvalue: 60
Modeling #3Software: Chimera, refmac / Refinement protocol: flexible / Target criteria: R-factor, FSC / Refinement space: RECIPROCAL
Input PDB model: 3U5D
Overall bvalue: 60
Modeling #4Software: Chimera, refmac / Refinement protocol: flexible / Target criteria: R-factor, FSC / Refinement space: RECIPROCAL
Input PDB model: 3U5E
Overall bvalue: 60
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