[English] 日本語
Yorodumi
- PDB-4v91: Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v91
TitleKluyveromyces lactis 80S ribosome in complex with CrPV-IRES
Components
  • 25S RRNA
  • 5.8S RRNA5.8S ribosomal RNA
  • 5S RRNA5S ribosomal RNA
  • EL13
  • EL14
  • EL15List of Subaru engines
  • EL18
  • EL19
  • EL20
  • EL21
  • EL22
  • EL24
  • EL27
  • EL29
  • EL30
  • EL31
  • EL32CD59
  • EL33
  • EL34
  • EL36
  • EL37
  • EL38
  • EL39
  • EL40
  • EL41
  • EL42
  • EL43
  • EL6
  • EL8
  • UL1
  • UL13
  • UL14
  • UL15
  • UL16
  • UL18
  • UL2
  • UL22
  • UL23
  • UL24
  • UL29
  • UL3
  • UL30
  • UL4
  • UL5
  • UL6
KeywordsRIBOSOME / TRANSLATION / INITIATION / IRES
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesKLUYVEROMYCES LACTIS (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsFernandez, I.S. / Bai, X. / Scheres, S.H.W. / 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.
History
DepositionMar 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4CUV, 4CUW
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Apr 22, 2015Group: Other
Revision 2.0Aug 2, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / em_software ...atom_site / em_software / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id
Revision 2.1Dec 11, 2019Group: Other / Category: atom_sites / pdbx_database_status
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] / _pdbx_database_status.process_site

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-2599
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2599
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: 25S RRNA
3: 5S RRNA
4: 5.8S RRNA
A: UL2
B: UL3
C: UL4
D: UL18
E: EL6
F: UL30
G: EL8
H: UL6
I: UL16
J: UL5
L: EL13
M: EL14
N: EL15
O: UL13
P: UL22
Q: EL18
R: EL19
S: EL20
T: EL21
U: EL22
V: UL14
W: EL24
X: UL23
Y: UL24
Z: EL27
a: UL15
b: EL29
c: EL30
d: EL31
e: EL32
f: EL33
g: EL34
h: UL29
i: EL36
j: EL37
k: EL38
l: EL39
m: EL40
n: EL41
o: EL42
p: EL43
t: UL1


Theoretical massNumber of molelcules
Total (without water)1,977,85945
Polymers1,977,85945
Non-polymers00
Water0
1


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

-
Components

-
RNA chain , 3 types, 3 molecules 134

#1: RNA chain 25S RRNA


Mass: 1097866.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#2: RNA chain 5S RRNA / 5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#3: RNA chain 5.8S RRNA / 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KLUYVEROMYCES LACTIS (yeast)

+
Protein , 41 types, 41 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#4: Protein UL2


Mass: 27463.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL2 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#5: Protein UL3


Mass: 43850.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL3 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#6: Protein UL4


Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL4 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#7: Protein UL18


Mass: 33764.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL18 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#8: Protein EL6


Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL6 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#9: Protein UL30


Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL30 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#10: Protein EL8


Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL8 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#11: Protein UL6


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL6 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#12: Protein UL16


Mass: 25410.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL16 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#13: Protein UL5


Mass: 19755.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL5 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#14: Protein EL13


Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL13 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#15: Protein EL14


Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL14 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#16: Protein EL15 / List of Subaru engines


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL15 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#17: Protein UL13


Mass: 44476.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL13 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#18: Protein UL22


Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL2 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#19: Protein EL18


Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL18 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#20: Protein EL19


Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL19 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#21: Protein EL20


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL20 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#22: Protein EL21 /


Mass: 18279.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL21 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#23: Protein EL22


Mass: 13711.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL22 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#24: Protein UL14


Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL14 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#25: Protein EL24


Mass: 17661.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL24 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#26: Protein UL23


Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL23 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#27: Protein UL24


Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL24 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#28: Protein EL27


Mass: 15568.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL27 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#29: Protein UL15


Mass: 16761.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL15 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#30: Protein EL29


Mass: 6691.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL29 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#31: Protein EL30


Mass: 11430.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL30 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#32: Protein EL31


Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL31 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#33: Protein EL32 / CD59


Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL32 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#34: Protein EL33


Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL33 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#35: Protein EL34 /


Mass: 13673.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL34 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#36: Protein UL29


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL29 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#37: Protein EL36


Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL36 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#38: Protein EL37


Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL37 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#39: Protein EL38


Mass: 8845.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL38 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#40: Protein EL39


Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL39 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#41: Protein EL40


Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL40 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#43: Protein EL42


Mass: 12246.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL42 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#44: Protein EL43


Mass: 10112.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL43 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#45: Protein UL1


Mass: 24524.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN UL1 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)

-
Protein/peptide , 1 types, 1 molecules n

#42: Protein/peptide EL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL41 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES
Type: RIBOSOME
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: PROPANE / Details: LIQUID ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 7, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 47000 X / Nominal defocus max: 3 nm / Nominal defocus min: 1.8 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 1900
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1REFMACmodel fitting
2UCSF Chimeramodel fitting
3RELION3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: RELIONList of Walmart brands / Resolution: 3.7 Å / Num. of particles: 18132 / Nominal pixel size: 1.34 Å / Symmetry type: POINT
Atomic model buildingB value: 60 / Protocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: R-FACTOR, FSC / Details: METHOD--FLEXIBLE
Atomic model buildingPDB-ID: 3B31

3b31

RefinementHighest resolution: 3.7 Å
Refinement stepCycle: LAST / Highest resolution: 3.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 74446 0 0 74446

+
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