[English] 日本語
Yorodumi
- PDB-5xxb: Large subunit of Toxoplasma gondii ribosome -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5xxb
TitleLarge subunit of Toxoplasma gondii ribosome
Components
  • (Ribosomal protein ...) x 41
  • 25S RNA
  • 5.8S RNA
  • 5S RNA5S ribosomal RNA
KeywordsRIBOSOME / parasitic ribosome / rRNA / rproteins
Specimen sourceToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.17 Å resolution
AuthorsLi, Z. / Guo, Q. / Zheng, L. / Ji, Y. / Xie, Y. / Lai, D. / Lun, Z. / Suo, X. / Gao, N.
CitationJournal: Cell Res. / Year: 2017
Title: Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii.
Authors: Zhifei Li / Qiang Guo / Lvqin Zheng / Yongsheng Ji / Yi-Ting Xie / De-Hua Lai / Zhao-Rong Lun / Xun Suo / Ning Gao
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 3, 2017 / Release: Aug 30, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 30, 2017Structure modelrepositoryInitial release
1.1Oct 18, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6778
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: 25S RNA
3: 5S RNA
4: 5.8S RNA
A: Ribosomal protein uL2
B: Ribosomal protein uL3
C: Ribosomal protein uL4
D: Ribosomal protein uL18
E: Ribosomal protein eL6
F: Ribosomal protein uL30
G: Ribosomal protein eL8
H: Ribosomal protein uL6
I: Ribosomal protein uL16
J: Ribosomal protein uL5
K: Ribosomal protein eL13
L: Ribosomal protein eL14
M: Ribosomal protein eL15
N: Ribosomal protein uL13
O: Ribosomal protein uL22
P: Ribosomal protein eL18
Q: Ribosomal protein eL19
R: Ribosomal protein eL20
S: Ribosomal protein eL21
T: Ribosomal protein eL22
U: Ribosomal protein uL14
V: Ribosomal protein eL24
W: Ribosomal protein uL23
X: Ribosomal protein uL24
Y: Ribosomal protein eL27
Z: Ribosomal protein uL15
a: Ribosomal protein eL29
b: Ribosomal protein eL30
c: Ribosomal protein eL31
d: Ribosomal protein eL32
e: Ribosomal protein eL33
f: Ribosomal protein eL34
g: Ribosomal protein uL29
h: Ribosomal protein eL36
i: Ribosomal protein eL37
j: Ribosomal protein eL38
k: Ribosomal protein eL39
l: Ribosomal protein eL40
n: Ribosomal protein eL42
o: Ribosomal protein eL43
p: Ribosomal protein eL28


Theoretical massNumber of molelcules
Total (without water)2,027,34644
Polyers2,027,34644
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)361790
ΔGint (kcal/M)-3074
Surface area (Å2)621290

-
Components

-
RNA chain , 3 types, 3 molecules 134

#1: RNA chain 25S RNA


Mass: 1120153.125 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#2: RNA chain 5S RNA / 5S ribosomal RNA


Mass: 39921.641 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#3: RNA chain 5.8S RNA


Mass: 50787.980 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)

+
Ribosomal protein ... , 41 types, 41 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#4: Protein/peptide Ribosomal protein uL2 /


Mass: 28314.898 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#5: Protein/peptide Ribosomal protein uL3 /


Mass: 44150.738 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#6: Protein/peptide Ribosomal protein uL4 /


Mass: 45837.258 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#7: Protein/peptide Ribosomal protein uL18 /


Mass: 35408.742 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#8: Protein/peptide Ribosomal protein eL6 /


Mass: 21563.535 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#9: Protein/peptide Ribosomal protein uL30 /


Mass: 30187.777 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#10: Protein/peptide Ribosomal protein eL8 /


Mass: 31095.934 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#11: Protein/peptide Ribosomal protein uL6 /


Mass: 21459.178 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#12: Protein/peptide Ribosomal protein uL16 /


Mass: 24846.014 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#13: Protein/peptide Ribosomal protein uL5 /


Mass: 20240.361 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#14: Protein/peptide Ribosomal protein eL13 /


Mass: 39757.371 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#15: Protein/peptide Ribosomal protein eL14 /


Mass: 15492.432 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#16: Protein/peptide Ribosomal protein eL15 /


Mass: 24387.846 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#17: Protein/peptide Ribosomal protein uL13 /


Mass: 31757.688 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#18: Protein/peptide Ribosomal protein uL22 /


Mass: 22319.188 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#19: Protein/peptide Ribosomal protein eL18 /


Mass: 21223.158 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#20: Protein/peptide Ribosomal protein eL19 /


Mass: 22221.574 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#21: Protein/peptide Ribosomal protein eL20 /


Mass: 21372.252 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#22: Protein/peptide Ribosomal protein eL21 /


Mass: 17932.977 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#23: Protein/peptide Ribosomal protein eL22 /


Mass: 15103.659 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#24: Protein/peptide Ribosomal protein uL14 /


Mass: 14842.553 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#25: Protein/peptide Ribosomal protein eL24 /


Mass: 17644.857 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#26: Protein/peptide Ribosomal protein uL23 /


Mass: 18600.809 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#27: Protein/peptide Ribosomal protein uL24 /


Mass: 16353.228 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#28: Protein/peptide Ribosomal protein eL27 /


Mass: 16841.355 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#29: Protein/peptide Ribosomal protein uL15 /


Mass: 16384.355 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#30: Protein/peptide Ribosomal protein eL29 /


Mass: 6387.679 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#31: Protein/peptide Ribosomal protein eL30 /


Mass: 11682.658 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#32: Protein/peptide Ribosomal protein eL31 /


Mass: 14389.729 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#33: Protein/peptide Ribosomal protein eL32 /


Mass: 15652.334 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#34: Protein/peptide Ribosomal protein eL33 /


Mass: 12873.091 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#35: Protein/peptide Ribosomal protein eL34 /


Mass: 15427.309 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#36: Protein/peptide Ribosomal protein uL29 /


Mass: 14231.108 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#37: Protein/peptide Ribosomal protein eL36 /


Mass: 11437.687 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#38: Protein/peptide Ribosomal protein eL37 /


Mass: 11256.210 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#39: Protein/peptide Ribosomal protein eL38 /


Mass: 9606.386 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#40: Protein/peptide Ribosomal protein eL39 /


Mass: 6172.519 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#41: Protein/peptide Ribosomal protein eL40 /


Mass: 14714.291 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#42: Protein/peptide Ribosomal protein eL42 /


Mass: 12098.689 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#43: Protein/peptide Ribosomal protein eL43 /


Mass: 10426.384 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)
#44: Protein/peptide Ribosomal protein eL28 /


Mass: 14787.717 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii (eukaryote)

-
Details

Sequence detailsSequences used in this study were derived from Toxoplasma gondii RH strain, which were not ...Sequences used in this study were derived from Toxoplasma gondii RH strain, which were not available at UNIPROT at the time of data processing.

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Large subunit of Toxoplasma gondii ribosome / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44
Source: NATURAL
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 108162 / Symmetry type: POINT

+
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