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Large subunit of Trichomonas vaginalis ribosome

by single particle reconstruction, at 3.2 A resolution

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#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-6784, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 5xy3
TitleLarge subunit of Trichomonas vaginalis ribosome
DescriptorUncharacterized protein
Ribosomal protein
Ubiquitin
putative/RNA Complex
(Ribosomal protein ...) x 23
(60S ribosomal protein ...) x 11
KeywordsRIBOSOME, Trichomonas vaginalis ribosome, rRNA, rprotein
AuthorsLi, Z., Guo, Q., Zheng, L., Ji, Y., Xie, Y., Lai, D., Lun, Z., Suo, X., Gao, N.
DateDeposition: 2017-07-06, Release: 2017-08-30
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-6784, Imaged by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-6784

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Cite: data citing same article

Fit: target map of fitting

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Article
Citation - primary
ArticleCell Res., Year 2017
TitleCryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii.
AuthorsZhifei Li, Qiang Guo, Lvqin Zheng, Yongsheng Ji, Yi-Ting Xie, De-Hua Lai, Zhao-Rong Lun, Xun Suo, Ning Gao
State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China.
Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonoses, Department of Microbiology and Parasitology, Anhui Medical University, Hefei, Anhui 230022, China.
Center for Parasitic Organisms, State Key Laboratory of Biocontrol, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China.
State Key Laboratory of Agrobiotechnology &National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
LinksPubMed: 28809395, DOI: 10.1038/cr.2017.104
Components
ID 1 : 25S ribosomal RNA
Description25S ribosomal RNA
Typepolyribonucleotide
Formula weight892223.312 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 2765
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksGenBank: 7243609, Sequence view
ID 2 : 5S ribosomal RNA
Description5S ribosomal RNA
Typepolyribonucleotide
Formula weight37963.594 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 118
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksGenBank: 68235680, Sequence view
ID 3 : 5.8S ribosomal RNA
Description5.8S ribosomal RNA
Typepolyribonucleotide
Formula weight52173.945 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 162
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksGenBank: 461415, Sequence view
ID 4 : uL2
DescriptionRibosomal protein L8, putative
Typepolypeptide(L)
Formula weight26949.082 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 251
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2E6Z8, Sequence view
ID 5 : uL3
DescriptionUncharacterized protein
Typepolypeptide(L)
Formula weight46904.270 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 415
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DD62, Sequence view
ID 6 : uL4
DescriptionRibosomal protein, putative
Typepolypeptide(L)
Formula weight40320.738 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 370
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2E4D0, Sequence view
ID 7 : uL18
DescriptionRibosomal protein L5
Typepolypeptide(L)
Formula weight34932.766 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 308
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DNM5, Sequence view
ID 8 : eL6
Description60S ribosomal protein L6, putative
Typepolypeptide(L)
Formula weight16045.772 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 151
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2FXW1, Sequence view
ID 9 : uL30
DescriptionRibosomal protein L30p/L7e, putative
Typepolypeptide(L)
Formula weight26842.281 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 239
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2F592, Sequence view
ID 10 : eL8
DescriptionRibosomal protein L7Ae, putative
Typepolypeptide(L)
Formula weight27602.273 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 244
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2ET60, Sequence view
ID 11 : uL6
DescriptionRibosomal protein L6, putative
Typepolypeptide(L)
Formula weight22930.506 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 197
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DDT1, Sequence view
ID 12 : uL16
DescriptionRibosomal protein, putative
Typepolypeptide(L)
Formula weight23800.781 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 209
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2FVZ6, Sequence view
ID 13 : uL5
Description60S ribosomal protein L11, putative
Typepolypeptide(L)
Formula weight19373.488 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 169
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2E7L8, Sequence view
ID 14 : eL13
DescriptionRibosomal protein L13e, putative
Typepolypeptide(L)
Formula weight21865.705 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 189
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2G4E1, Sequence view
ID 15 : eL14
DescriptionRibosomal protein L14, putative
Typepolypeptide(L)
Formula weight14726.112 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 128
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DZ49, Sequence view
ID 16 : eL15
DescriptionRibosomal protein L15
Typepolypeptide(L)
Formula weight24323.465 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 204
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2ECR7, Sequence view
ID 17 : uL13
DescriptionRibosomal protein L13, putative
Typepolypeptide(L)
Formula weight22569.111 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 200
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DZ26, Sequence view
ID 18 : uL22
DescriptionRibosomal protein L22, putative
Typepolypeptide(L)
Formula weight18530.490 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 164
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DM53, Sequence view
ID 19 : eL18
Description60S ribosomal protein L18, putative
Typepolypeptide(L)
Formula weight21122.545 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 186
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2D7Q5, Sequence view
ID 20 : eL19
Description60S ribosomal protein L19-3, putative
Typepolypeptide(L)
Formula weight21056.785 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 178
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2D8G1, Sequence view
ID 21 : eL20
Description60S ribosomal protein L18a
Typepolypeptide(L)
Formula weight19853.973 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 176
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2EP03, Sequence view
ID 22 : eL21
DescriptionRibosomal protein L21e, putative
Typepolypeptide(L)
Formula weight17910.867 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 159
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2F2S5, Sequence view
ID 23 : eL22
Description60S ribosomal protein L22-1, putative
Typepolypeptide(L)
Formula weight12237.054 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 106
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DNV5, Sequence view
ID 24 : uL14
Description60S ribosomal protein L23, putative
Typepolypeptide(L)
Formula weight14840.554 Da
Number of molecules1
ID24
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 140
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DP51, Sequence view
ID 25 : eL24
DescriptionRibosomal protein L24e, putative
Typepolypeptide(L)
Formula weight13282.475 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 113
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DJQ1, Sequence view
ID 26 : uL23
DescriptionRibosomal protein L23, putative
Typepolypeptide(L)
Formula weight15582.249 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 140
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DUV8, Sequence view
ID 27 : uL24
DescriptionRibosomal protein L24, putative
Typepolypeptide(L)
Formula weight15782.617 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 138
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DKF2, Sequence view
ID 28 : eL27
DescriptionRibosomal protein L27e, putative
Typepolypeptide(L)
Formula weight15946.061 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 139
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DNC1, Sequence view
ID 29 : uL15
DescriptionUncharacterized protein
Typepolypeptide(L)
Formula weight17006.787 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 151
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DHU7, Sequence view
ID 30 : eL29
Description60S ribosomal protein L29
Typepolypeptide(L)
Formula weight6823.724 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 58
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DM33, Sequence view
ID 31 : eL30
Description60S ribosomal protein L30, putative
Typepolypeptide(L)
Formula weight12316.229 Da
Number of molecules1
ID31
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 112
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2E6Z9, Sequence view
ID 32 : eL31
DescriptionRibosomal protein L31e, putative
Typepolypeptide(L)
Formula weight12446.528 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 110
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2D9N8, Sequence view
ID 33 : eL32
DescriptionRibosomal protein L32, putative
Typepolypeptide(L)
Formula weight15249.669 Da
Number of molecules1
ID33
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 132
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2F2J0, Sequence view
ID 34 : eL33
DescriptionRibosomal protein L35Ae, putative
Typepolypeptide(L)
Formula weight11668.678 Da
Number of molecules1
ID34
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 102
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DSF3, Sequence view
ID 35 : eL34
DescriptionRibosomal protein L34e, putative
Typepolypeptide(L)
Formula weight13346.646 Da
Number of molecules1
ID35
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 116
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2FWA1, Sequence view
ID 36 : uL29
DescriptionRibosomal protein L29, putative
Typepolypeptide(L)
Formula weight14300.049 Da
Number of molecules1
ID36
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 124
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2E6R2, Sequence view
ID 37 : eL36
DescriptionRibosomal protein L36e, putative
Typepolypeptide(L)
Formula weight10941.717 Da
Number of molecules1
ID37
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 91
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2EXW7, Sequence view
ID 38 : eL37
DescriptionRibosomal protein L37
Typepolypeptide(L)
Formula weight9355.945 Da
Number of molecules1
ID38
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 81
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2F8Y8, Sequence view
ID 39 : eL38
DescriptionRibosomal protein L38e, putative
Typepolypeptide(L)
Formula weight8468.960 Da
Number of molecules1
ID39
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 74
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2FFH9, Sequence view
ID 40 : eL39
Description60S ribosomal protein L39, putative
Typepolypeptide(L)
Formula weight6297.775 Da
Number of molecules1
ID40
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 51
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2D9N4, Sequence view
ID 41 : eL40
DescriptionUbiquitin, putative
Typepolypeptide(L)
FragmentUNP residues 35-166
Formula weight15101.515 Da
Number of molecules1
ID41
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 132
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DGL5, Sequence view
ID 42 : eL41
Description60S ribosomal protein L44, putative
Typepolypeptide(L)
Formula weight12471.015 Da
Number of molecules1
ID42
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 104
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DAI6, Sequence view
ID 43 : eL43
DescriptionUncharacterized protein
Typepolypeptide(L)
Formula weight10051.994 Da
Number of molecules1
ID43
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 92
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DEM7, Sequence view
Sample
Entity assembly
Entity id list1, 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
NameLarge subunit of Trichomonas vaginalis ribosome
SourceNATURAL
TypeRIBOSOME
Buffer
Specimen id1
PH7.4
Experiment
Aggregation statePARTICLE
Reconstruction methodSINGLE PARTICLE
Vitrification
Specimen id1
Cryogen nameETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TITAN KRIOS
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
Processing
3D reconstruction
Image processing id1
Number of particles57162
Resolution3.2 A
Resolution methodFSC 0.143 CUT-OFF
Symmetry typePOINT
Download
PDB format
Allpdb5xy3.ent.gz
pdb5xy3.ent (uncompressed file)
Header onlypdb5xy3.ent.gz
mmCIF format
mmCIF5xy3.cif.gz
XML format
All5xy3.xml.gz
No-atom5xy3-noatom.xml.gz
Ext-atom5xy3-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 7.4 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 7.3 MB