[English] 日本語
Yorodumi
- PDB-5xxu: Small subunit of Toxoplasma gondii ribosome -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5xxu
TitleSmall subunit of Toxoplasma gondii ribosome
DescriptoruS2, eS1, uS5, uS3, eS4, uS7, eS6, eS7, eS8, uS4, eS10, uS17, eS12, uS15, uS11, uS19, uS9, eS17, uS13, eS19, uS10, eS21, uS8, uS12, eS24, eS25, eS26, eS27, eS28, uS14, eS30, eS31, eL41/RNA Complex
KeywordsRIBOSOME / Toxoplasma gondii ribosome / rRNA / rprotein
Specimen sourceToxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /
MethodElectron microscopy (3.35 Å resolution / Particle / Single particle)
AuthorsLI, Z. / Guo, Q. / Zheng, L. / Ji, Y. / Xie, Y. / Lai, D. / Lun, Z. / Suo, X. / Gao, N.
CitationCell Res., 2017, 27, 1275-1288

Cell Res., 2017, 27, 1275-1288 Yorodumi Papers
Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii.
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 5, 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
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
2: 18S RNA
A: Ribosomal protein uS2
B: Ribosomal protein eS1
C: Ribosomal protein uS5
D: Ribosomal protein uS3
E: Ribosomal protein eS4
F: Ribosomal protein uS7
G: Ribosomal protein eS6
H: Ribosomal protein eS7
I: Ribosomal protein eS8
J: Ribosomal protein uS4
K: Ribosomal protein eS10
L: Ribosomal protein uS17
M: Ribosomal protein eS12
N: Ribosomal protein uS15
O: Ribosomal protein uS11
P: Ribosomal protein uS19
Q: Ribosomal protein uS9
R: Ribosomal protein eS17
S: Ribosomal protein uS13
T: Ribosomal protein eS19
U: Ribosomal protein uS10
V: Ribosomal protein eS21
W: Ribosomal protein uS8
X: Ribosomal protein uS12
Y: Ribosomal protein eS24
Z: Ribosomal protein eS25
a: Ribosomal protein eS26
b: Ribosomal protein eS27
c: Ribosomal protein eS28
d: Ribosomal protein uS14
e: Ribosomal protein eS30
f: Ribosomal protein eS31
m: Ribosomal protein eL41


Theoretical massNumber of molelcules
Total (without water)1,177,11334
Polyers1,177,11334
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)181100
ΔGint (kcal/M)-1347
Surface area (Å2)381840

-
Components

-
RNA chain , 1 types, 1 molecules 2

#1: RNA chain18S RNA


Mass: 576630.812 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii

+
Ribosomal protein ... , 33 types, 33 molecules ABCDEFGHIJ...

#2: Polypeptide(L)Ribosomal protein uS2


Mass: 31546.902 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#3: Polypeptide(L)Ribosomal protein eS1


Mass: 29425.625 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#4: Polypeptide(L)Ribosomal protein uS5


Mass: 29385.004 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#5: Polypeptide(L)Ribosomal protein uS3


Mass: 26117.539 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#6: Polypeptide(L)Ribosomal protein eS4


Mass: 30204.713 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#7: Polypeptide(L)Ribosomal protein uS7


Mass: 21650.238 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#8: Polypeptide(L)Ribosomal protein eS6


Mass: 29027.504 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#9: Polypeptide(L)Ribosomal protein eS7


Mass: 22631.727 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#10: Polypeptide(L)Ribosomal protein eS8


Mass: 23615.604 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#11: Polypeptide(L)Ribosomal protein uS4


Mass: 21731.396 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#12: Polypeptide(L)Ribosomal protein eS10


Mass: 17428.098 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#13: Polypeptide(L)Ribosomal protein uS17


Mass: 18715.984 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#14: Polypeptide(L)Ribosomal protein eS12


Mass: 15419.675 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#15: Polypeptide(L)Ribosomal protein uS15


Mass: 17211.363 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#16: Polypeptide(L)Ribosomal protein uS11


Mass: 16330.598 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#17: Polypeptide(L)Ribosomal protein uS19


Mass: 17190.223 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#18: Polypeptide(L)Ribosomal protein uS9


Mass: 16587.488 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#19: Polypeptide(L)Ribosomal protein eS17


Mass: 15256.675 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#20: Polypeptide(L)Ribosomal protein uS13


Mass: 17761.662 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#21: Polypeptide(L)Ribosomal protein eS19


Mass: 18414.312 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#22: Polypeptide(L)Ribosomal protein uS10


Mass: 25943.293 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#23: Polypeptide(L)Ribosomal protein eS21


Mass: 9049.265 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#24: Polypeptide(L)Ribosomal protein uS8


Mass: 14973.676 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#25: Polypeptide(L)Ribosomal protein uS12


Mass: 15837.605 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#26: Polypeptide(L)Ribosomal protein eS24


Mass: 15230.910 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#27: Polypeptide(L)Ribosomal protein eS25


Mass: 18707.014 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#28: Polypeptide(L)Ribosomal protein eS26


Mass: 12753.630 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#29: Polypeptide(L)Ribosomal protein eS27


Mass: 9105.850 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#30: Polypeptide(L)Ribosomal protein eS28


Mass: 7601.858 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#31: Polypeptide(L)Ribosomal protein uS14


Mass: 6533.824 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#32: Polypeptide(L)Ribosomal protein eS30


Mass: 6619.800 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#33: Polypeptide(L)Ribosomal protein eS31


Mass: 17353.152 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#34: Polypeptide(L)Ribosomal protein eL41


Mass: 5120.324 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii

-
Details

Sequence detailsSequences 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

-
Sample preparation

ComponentName: Small 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
Source: NATURAL
Source (natural)Organism: Toxoplasma gondii
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
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: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 108162 / Symmetry type: POINT
Least-squares processHighest resolution: 3.35 Å

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more