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Small subunit of Trichomonas vaginalis ribosome

by single particle reconstruction, at 3.35 A resolution

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#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-6788, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 5xyi
TitleSmall subunit of Trichomonas vaginalis ribosome
DescriptorUncharacterized protein
Plectin/S10 domain containing protein
Guanine nucleotide-binding protein beta subunit
eL41/RNA Complex
(40S ribosomal protein ...) x 15
(Ribosomal protein ...) x 10
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: 2017-07-08, 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-6788, Imaged by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-6788

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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 : 18S
Description18S
Typepolyribonucleotide
Formula weight508656.188 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: 1577
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksSequence view
ID 2 : uS2
Description40S ribosomal protein SA
Typepolypeptide(L)
Formula weight28584.676 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: 256
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2EFE7, Sequence view
ID 3 : eS1
DescriptionRibosomal protein S3Ae, putative
Typepolypeptide(L)
Formula weight28085.471 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: 247
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2G9Z8, Sequence view
ID 4 : uS5
DescriptionUncharacterized protein
Typepolypeptide(L)
Formula weight30083.736 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: 272
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2EHK3, Sequence view
ID 5 : uS3
DescriptionRibosomal protein S3, putative
Typepolypeptide(L)
Formula weight24505.658 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: 216
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DIM3, Sequence view
ID 6 : eS4
Description40S ribosomal protein S4
Typepolypeptide(L)
Formula weight28589.561 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: 255
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2FC75, Sequence view
ID 7 : uS7
Description40s ribosomal protein S5-B, putative
Typepolypeptide(L)
Formula weight21672.889 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: 193
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2E4S6, Sequence view
ID 8 : eS6
Description40S ribosomal protein S6
Typepolypeptide(L)
Formula weight24583.883 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: 216
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DEJ9, Sequence view
ID 9 : eS7
Description40S ribosomal protein S7, putative
Typepolypeptide(L)
Formula weight18708.568 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: 168
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2G5X6, Sequence view
ID 10 : eS8
Description40S ribosomal protein S8
Typepolypeptide(L)
Formula weight22118.488 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: 197
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2E1L5, Sequence view
ID 11 : uS4
DescriptionUncharacterized protein
Typepolypeptide(L)
Formula weight21811.295 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: 185
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DNY3, Sequence view
ID 12 : eS10
DescriptionPlectin/S10 domain containing protein
Typepolypeptide(L)
Formula weight16251.438 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: 141
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2EBA2, Sequence view
ID 13 : uS17
DescriptionUncharacterized protein
Typepolypeptide(L)
Formula weight18015.252 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: 155
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DHU8, Sequence view
ID 14 : eS12
DescriptionRibosomal protein L7Ae, putative
Typepolypeptide(L)
Formula weight13714.954 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: 124
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2FA40, Sequence view
ID 15 : uS15
Description40S ribosomal protein S13, putative
Typepolypeptide(L)
Formula weight17071.031 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: 151
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2D9L2, Sequence view
ID 16 : uS11
DescriptionRibosomal protein S14
Typepolypeptide(L)
Formula weight16689.012 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: 159
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: Q76KS8, Sequence view
ID 17 : uS19
DescriptionRibosomal protein S19, putative
Typepolypeptide(L)
Formula weight16286.080 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: 144
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DVD8, Sequence view
ID 18 : uS9
Description40S ribosomal protein S16, putative
Typepolypeptide(L)
Formula weight15626.175 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: 140
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2D919, Sequence view
ID 19 : eS17
Description40S ribosomal protein S17-B, putative
Typepolypeptide(L)
Formula weight14964.434 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: 129
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DPS3, Sequence view
ID 20 : uS13
DescriptionRibosomal protein S13p/S18e, putative
Typepolypeptide(L)
Formula weight17564.523 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: 155
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DTR8, Sequence view
ID 21 : eS19
DescriptionRibosomal protein S19e, putative
Typepolypeptide(L)
Formula weight16584.188 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: 148
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2EG54, Sequence view
ID 22 : uS10
DescriptionRibosomal protein S10p/S20e, putative
Typepolypeptide(L)
Formula weight13933.201 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: 123
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2FDE0, Sequence view
ID 23 : eS21
Description40S ribosomal protein S21
Typepolypeptide(L)
Formula weight9853.130 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: 89
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2FFS8, Sequence view
ID 24 : uS8
DescriptionRibosomal protein S15a
Typepolypeptide(L)
Formula weight14583.213 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: 130
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DLW4, Sequence view
ID 25 : uS12
Description40S ribosomal protein S23, putative
Typepolypeptide(L)
Formula weight15592.457 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: 144
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2D895, Sequence view
ID 26 : eS24
DescriptionRibosomal protein S24e, putative
Typepolypeptide(L)
Formula weight16069.884 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: A2F0H5, Sequence view
ID 27 : eS25
DescriptionUncharacterized protein
Typepolypeptide(L)
Formula weight12645.859 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: 115
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2ER97, Sequence view
ID 28 : eS26
Description40S ribosomal protein S26
Typepolypeptide(L)
Formula weight13889.256 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: 118
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DST7, Sequence view
ID 29 : eS27
Description40S ribosomal protein S27
Typepolypeptide(L)
Formula weight9467.907 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: 86
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2FBZ2, Sequence view
ID 30 : eS28
DescriptionUncharacterized protein
Typepolypeptide(L)
Formula weight7650.717 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: 68
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DQN8, Sequence view
ID 31 : uS14
Description40S ribosomal protein S29, putative
Typepolypeptide(L)
Formula weight6843.100 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: 57
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2DYA8, Sequence view
ID 32 : eS30
Description40S ribosomal protein S30
Typepolypeptide(L)
Formula weight6919.079 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: 62
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2FHY5, Sequence view
ID 33 : RACK1
DescriptionGuanine nucleotide-binding protein beta subunit, putative
Typepolypeptide(L)
Formula weight37151.832 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: 335
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksUniProt: A2ELV7, Sequence view
ID 34 : eL41
DescriptioneL41
Typepolypeptide(L)
Formula weight3354.243 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: 25
NCBI taxonomy: ID:5722
Organism scientific: Trichomonas vaginalis
LinksSequence 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
NameSmall 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
Resolution3.35 A
Resolution methodFSC 0.143 CUT-OFF
Symmetry typePOINT
Download
PDB format
Allpdb5xyi.ent.gz
pdb5xyi.ent (uncompressed file)
Header onlypdb5xyi.ent.gz
mmCIF format
mmCIF5xyi.cif.gz
XML format
All5xyi.xml.gz
No-atom5xyi-noatom.xml.gz
Ext-atom5xyi-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 6.7 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 6.7 MB