[English] 日本語
Yorodumi
- PDB-5xy3: Large subunit of Trichomonas vaginalis ribosome -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5xy3
TitleLarge subunit of Trichomonas vaginalis ribosome
Components
  • (60S ribosomal protein ...) x 11
  • (Ribosomal protein ...) x 23
  • (Ribosomal protein, ...) x 2
  • (Uncharacterized ...) x 3
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Ubiquitin, putative
KeywordsRIBOSOME / Trichomonas vaginalis ribosome / rRNA / rprotein
Function / homologyRibosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Ribosomal protein L32e superfamily / 50S ribosomal protein L30e-like ...Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Ribosomal protein L32e superfamily / 50S ribosomal protein L30e-like / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / Ubiquitin-like domain superfamily / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L22p/L17e / Ribosomal protein L5 domain superfamily / Ubiquitin conserved site / Ubiquitin / Ribosomal protein L14P, conserved site / Ribosomal protein L18e/L15P / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L30e, conserved site / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L4 domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L15e core domain superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L14p/L23e / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal L27e protein family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L19e / Ribosomal protein L13e / Ribosomal protein L32 / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L22e protein family / Ribosomal L29e protein family / Ribosomal protein L24e / Ribosomal L37ae protein family / Ribosomal L38e protein family / Ribosomal protein L37e / Ribosomal protein L14 / Ribosomal Proteins L2, C-terminal domain / Ribosomal L30 N-terminal domain / Ribosomal L18 C-terminal region / Ribosomal protein L35Ae / Ribosomal protein L34e / Ubiquitin family / ribosomal L5P family C-terminus / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L3 / Ribosomal protein L30p/L7e / Ribosomal protein L13 / Ribosomal protein L4/L1 family / Ribosomal L15 / Ribosomal protein L31e / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L29 protein / Ribosomal L39 protein / Ribosomal protein L44 / Ribosomal L40e family / Ribosomal protein L21e / Ribosomal protein L36e / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L37e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L24e-related / Ribosomal protein L36e / Ribosomal protein L44e / Ribosomal protein L3 / Ubiquitin domain / Ribosomal protein L6 / 60S ribosomal protein L6E / Ribosomal protein L22/L17 / Ribosomal protein L30e / Ribosomal protein L27e / Ribosomal protein L21e / Ribosomal protein L15, conserved site / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L29, conserved site / Ribosomal protein L15e / Ribosomal protein L14P / Ribosomal protein L35A / Ribosomal protein L29 signature. / Ubiquitin domain profile. / Ribosomal protein L21e signature.
Function and homology information
Specimen sourceTrichomonas vaginalis (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 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
Abstract: As an indispensable molecular machine universal in all living organisms, the ribosome has been selected by evolution to be the natural target of many antibiotics and small-molecule inhibitors. ...As an indispensable molecular machine universal in all living organisms, the ribosome has been selected by evolution to be the natural target of many antibiotics and small-molecule inhibitors. High-resolution structures of pathogen ribosomes are crucial for understanding the general and unique aspects of translation control in disease-causing microbes. With cryo-electron microscopy technique, we have determined structures of the cytosolic ribosomes from two human parasites, Trichomonas vaginalis and Toxoplasma gondii, at resolution of 3.2-3.4 Å. Although the ribosomal proteins from both pathogens are typical members of eukaryotic families, with a co-evolution pattern between certain species-specific insertions/extensions and neighboring ribosomal RNA (rRNA) expansion segments, the sizes of their rRNAs are sharply different. Very interestingly, rRNAs of T. vaginalis are in size comparable to prokaryotic counterparts, with nearly all the eukaryote-specific rRNA expansion segments missing. These structures facilitate the dissection of evolution path for ribosomal proteins and RNAs, and may aid in design of novel translation inhibitors.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 6, 2017 / Release: Aug 30, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 30, 2017Structure modelrepositoryInitial release
1.1Sep 6, 2017Structure modelStructure summaryentity_entity.pdbx_description
1.2Oct 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-6784
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
A: Ribosomal protein L8, putative
B: Uncharacterized protein
C: Ribosomal protein, putative
D: Ribosomal protein L5
E: 60S ribosomal protein L6, putative
F: Ribosomal protein L30p/L7e, putative
G: Ribosomal protein L7Ae, putative
H: Ribosomal protein L6, putative
I: Ribosomal protein, putative
J: 60S ribosomal protein L11, putative
L: Ribosomal protein L13e, putative
M: Ribosomal protein L14, putative
N: Ribosomal protein L15
O: Ribosomal protein L13, putative
P: Ribosomal protein L22, putative
Q: 60S ribosomal protein L18, putative
R: 60S ribosomal protein L19-3, putative
S: 60S ribosomal protein L18a
T: Ribosomal protein L21e, putative
U: 60S ribosomal protein L22-1, putative
V: 60S ribosomal protein L23, putative
W: Ribosomal protein L24e, putative
X: Ribosomal protein L23, putative
Y: Ribosomal protein L24, putative
Z: Ribosomal protein L27e, putative
a: Uncharacterized protein
b: 60S ribosomal protein L29
c: 60S ribosomal protein L30, putative
d: Ribosomal protein L31e, putative
e: Ribosomal protein L32, putative
f: Ribosomal protein L35Ae, putative
g: Ribosomal protein L34e, putative
h: Ribosomal protein L29, putative
i: Ribosomal protein L36e, putative
j: Ribosomal protein L37
k: Ribosomal protein L38e, putative
l: 60S ribosomal protein L39, putative
m: Ubiquitin, putative
o: 60S ribosomal protein L44, putative
p: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)1,713,54043
Polyers1,713,54043
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)308510
ΔGint (kcal/M)-2751
Surface area (Å2)556640

-
Components

+
RNA chain , 3 types, 3 molecules 134

#1: RNA chain 25S ribosomal RNA /


Mass: 892223.312 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: GenBank:7243609
#2: RNA chain 5S ribosomal RNA /


Mass: 37963.594 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: GenBank:68235680
#3: RNA chain 5.8S ribosomal RNA


Mass: 52173.945 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: GenBank:461415

+
Ribosomal protein ... , 23 types, 23 molecules ADFGHLMNOPTWXYZdefghijk

#4: Protein/peptide Ribosomal protein L8, putative / Ribosome / uL2


Mass: 26949.082 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2E6Z8
#7: Protein/peptide Ribosomal protein L5 / 60S ribosomal protein L5 / uL18


Mass: 34932.766 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DNM5
#9: Protein/peptide Ribosomal protein L30p/L7e, putative / Ribosome / uL30


Mass: 26842.281 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2F592
#10: Protein/peptide Ribosomal protein L7Ae, putative / Ribosome / eL8


Mass: 27602.273 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2ET60
#11: Protein/peptide Ribosomal protein L6, putative / Ribosome / uL6


Mass: 22930.506 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DDT1
#14: Protein/peptide Ribosomal protein L13e, putative / Ribosome / eL13


Mass: 21865.705 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2G4E1
#15: Protein/peptide Ribosomal protein L14, putative / Ribosome / eL14


Mass: 14726.112 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DZ49
#16: Protein/peptide Ribosomal protein L15 / Ribosome / eL15


Mass: 24323.465 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2ECR7
#17: Protein/peptide Ribosomal protein L13, putative / Ribosome / uL13


Mass: 22569.111 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DZ26
#18: Protein/peptide Ribosomal protein L22, putative / Ribosome / uL22


Mass: 18530.490 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DM53
#22: Protein/peptide Ribosomal protein L21e, putative / Ribosome / eL21


Mass: 17910.867 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2F2S5
#25: Protein/peptide Ribosomal protein L24e, putative / Ribosome / eL24


Mass: 13282.475 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DJQ1
#26: Protein/peptide Ribosomal protein L23, putative / Ribosome / uL23


Mass: 15582.249 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DUV8
#27: Protein/peptide Ribosomal protein L24, putative / Ribosome / uL24


Mass: 15782.617 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DKF2
#28: Protein/peptide Ribosomal protein L27e, putative / Ribosome / eL27


Mass: 15946.061 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DNC1
#32: Protein/peptide Ribosomal protein L31e, putative / Ribosome / eL31


Mass: 12446.528 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2D9N8
#33: Protein/peptide Ribosomal protein L32, putative / Ribosome / eL32


Mass: 15249.669 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2F2J0
#34: Protein/peptide Ribosomal protein L35Ae, putative / Ribosome / eL33


Mass: 11668.678 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DSF3
#35: Protein/peptide Ribosomal protein L34e, putative / Ribosome / eL34


Mass: 13346.646 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2FWA1
#36: Protein/peptide Ribosomal protein L29, putative / Ribosome / uL29


Mass: 14300.049 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2E6R2
#37: Protein/peptide Ribosomal protein L36e, putative / Ribosome / eL36


Mass: 10941.717 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2EXW7
#38: Protein/peptide Ribosomal protein L37 / Ribosome / eL37


Mass: 9355.945 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2F8Y8
#39: Protein/peptide Ribosomal protein L38e, putative / Ribosome / eL38


Mass: 8468.960 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2FFH9

+
Uncharacterized ... , 3 types, 3 molecules Bap

#5: Protein/peptide Uncharacterized protein / uL3


Mass: 46904.270 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DD62
#29: Protein/peptide Uncharacterized protein / uL15


Mass: 17006.787 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DHU7
#43: Protein/peptide Uncharacterized protein / eL43


Mass: 10051.994 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DEM7

+
Ribosomal protein, ... , 2 types, 2 molecules CI

#6: Protein/peptide Ribosomal protein, putative / Ribosome / uL4


Mass: 40320.738 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2E4D0
#12: Protein/peptide Ribosomal protein, putative / Ribosome / uL16


Mass: 23800.781 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2FVZ6

+
60S ribosomal protein ... , 11 types, 11 molecules EJQRSUVbclo

#8: Protein/peptide 60S ribosomal protein L6, putative / / eL6


Mass: 16045.772 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2FXW1
#13: Protein/peptide 60S ribosomal protein L11, putative / / uL5


Mass: 19373.488 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2E7L8
#19: Protein/peptide 60S ribosomal protein L18, putative / / eL18


Mass: 21122.545 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2D7Q5
#20: Protein/peptide 60S ribosomal protein L19-3, putative / / eL19


Mass: 21056.785 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2D8G1
#21: Protein/peptide 60S ribosomal protein L18a / / eL20


Mass: 19853.973 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2EP03
#23: Protein/peptide 60S ribosomal protein L22-1, putative / / eL22


Mass: 12237.054 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DNV5
#24: Protein/peptide 60S ribosomal protein L23, putative / / uL14


Mass: 14840.554 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DP51
#30: Protein/peptide 60S ribosomal protein L29 / / eL29


Mass: 6823.724 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DM33
#31: Protein/peptide 60S ribosomal protein L30, putative / / eL30


Mass: 12316.229 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2E6Z9
#40: Protein/peptide 60S ribosomal protein L39, putative / / eL39


Mass: 6297.775 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2D9N4
#42: Protein/peptide 60S ribosomal protein L44, putative / / eL41


Mass: 12471.015 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DAI6

+
Protein/peptide , 1 types, 1 molecules m

#41: Protein/peptide Ubiquitin, putative / / eL40


Mass: 15101.515 Da / Num. of mol.: 1 / Fragment: UNP residues 35-166 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt:A2DGL5

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Large subunit of Trichomonas vaginalis 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
Source: NATURAL
Source (natural)Organism: Trichomonas vaginalis (eukaryote)
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 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 57162 / 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.
  • 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.: 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