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

+
Open data


ID or keywords:

Loading...

no data

-
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
Specimen sourceKLUYVEROMYCES LACTIS (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 21, 2014 / Release: Jul 9, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 9, 2014Structure modelrepositoryInitial release
1.1Dec 10, 2014Structure modelOther
1.2Apr 22, 2015Structure modelOther
2.0Aug 2, 2017Structure modelAdvisory / Atomic model / Data collection / Derived calculationsatom_site / em_software / pdbx_unobs_or_zero_occ_atoms / struct_conn_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

-
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
Polyers1,977,85945
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: (natural) KLUYVEROMYCES LACTIS (yeast)
#2: RNA chain 5S RRNA / 5S ribosomal RNA


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


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)

+
Protein/peptide , 42 types, 42 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#4: Protein/peptide UL2


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 14583.077 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL40 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#42: Protein/peptide EL41


Mass: 3354.243 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL41 / Source: (natural) KLUYVEROMYCES LACTIS (yeast)
#43: Protein/peptide EL42


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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
MicroscopyMicroscope model: 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 / 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 scansNumber 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
3D reconstructionMethod: RELIONList of Walmart brands / Resolution: 3.7 Å / Number of particles: 18132 / Nominal pixel size: 1.34 / Symmetry type: POINT
Atomic model buildingDetails: METHOD--FLEXIBLE / Overall b value: 60 / Ref protocol: FLEXIBLE FIT / Ref space: RECIPROCAL / Target criteria: R-FACTOR, FSC
Atomic model buildingPDB-ID: 3B31
Least-squares processHighest resolution: 3.7 Å
Refine hist #LASTHighest resolution: 3.7 Å
Number of atoms included #LASTProtein: 0 / Nucleic acid: 74446 / Ligand: 0 / Solvent: 0 / Total: 74446

+
About Yorodumi

-
News

-
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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