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Large subunit of Toxoplasma gondii ribosome

by single particle reconstruction, at 3.17 A resolution

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#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-6778, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 5xxb
TitleLarge subunit of Toxoplasma gondii ribosome
DescriptoruL2, uL3, uL4, uL18, eL6, uL30, eL8, uL6, uL16, uL5, eL13, eL14, eL15, uL13, uL22, eL18, eL19, eL20, eL21, eL22, uL14, eL24, uL23, uL24, eL27, uL15, eL29, eL30, eL31, eL32, eL33, eL34, uL29, eL36, eL37, eL38, eL39, eL40, eL42, eL43, eL28/RNA Complex
KeywordsRIBOSOME, parasitic ribosome, rRNA, rproteins
AuthorsLi, Z., Guo, Q., Zheng, L., Ji, Y., Xie, Y., Lai, D., Lun, Z., Suo, X., Gao, N.
DateDeposition: 2017-07-03, Release: 2017-08-30
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
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.
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-6778, Imaged by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-6778

CiteFit

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 RNA
Description25S RNA
Typepolyribonucleotide
Formula weight1120153.125 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: 3477
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii

LinksSequence view
ID 2 : 5S RNA
Description5S RNA
Typepolyribonucleotide
Formula weight39921.641 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: 124
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 3 : 5.8S RNA
Description5.8S RNA
Typepolyribonucleotide
Formula weight50787.980 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: 158
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 4 : Ribosomal protein uL2
DescriptionRibosomal protein uL2
Typepolypeptide(L)
Formula weight28314.898 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: 260
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 5 : Ribosomal protein uL3
DescriptionRibosomal protein uL3
Typepolypeptide(L)
Formula weight44150.738 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: 389
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 6 : Ribosomal protein uL4
DescriptionRibosomal protein uL4
Typepolypeptide(L)
Formula weight45837.258 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: 416
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 7 : Ribosomal protein uL18
DescriptionRibosomal protein uL18
Typepolypeptide(L)
Formula weight35408.742 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: 310
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 8 : Ribosomal protein eL6
DescriptionRibosomal protein eL6
Typepolypeptide(L)
Formula weight21563.535 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: 193
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 9 : Ribosomal protein uL30
DescriptionRibosomal protein uL30
Typepolypeptide(L)
Formula weight30187.777 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: 258
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 10 : Ribosomal protein eL8
DescriptionRibosomal protein eL8
Typepolypeptide(L)
Formula weight31095.934 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: 276
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 11 : Ribosomal protein uL6
DescriptionRibosomal protein uL6
Typepolypeptide(L)
Formula weight21459.178 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: 190
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 12 : Ribosomal protein uL16
DescriptionRibosomal protein uL16
Typepolypeptide(L)
Formula weight24846.014 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: 221
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 13 : Ribosomal protein uL5
DescriptionRibosomal protein uL5
Typepolypeptide(L)
Formula weight20240.361 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: 175
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 14 : Ribosomal protein eL13
DescriptionRibosomal protein eL13
Typepolypeptide(L)
Formula weight39757.371 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: 355
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 15 : Ribosomal protein eL14
DescriptionRibosomal protein eL14
Typepolypeptide(L)
Formula weight15492.432 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: 134
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 16 : Ribosomal protein eL15
DescriptionRibosomal protein eL15
Typepolypeptide(L)
Formula weight24387.846 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: 205
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 17 : Ribosomal protein uL13
DescriptionRibosomal protein uL13
Typepolypeptide(L)
Formula weight31757.688 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: 269
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 18 : Ribosomal protein uL22
DescriptionRibosomal protein uL22
Typepolypeptide(L)
Formula weight22319.188 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: 195
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 19 : Ribosomal protein eL18
DescriptionRibosomal protein eL18
Typepolypeptide(L)
Formula weight21223.158 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: 187
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 20 : Ribosomal protein eL19
DescriptionRibosomal protein eL19
Typepolypeptide(L)
Formula weight22221.574 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: 187
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 21 : Ribosomal protein eL20
DescriptionRibosomal protein eL20
Typepolypeptide(L)
Formula weight21372.252 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: 183
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 22 : Ribosomal protein eL21
DescriptionRibosomal protein eL21
Typepolypeptide(L)
Formula weight17932.977 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: 157
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 23 : Ribosomal protein eL22
DescriptionRibosomal protein eL22
Typepolypeptide(L)
Formula weight15103.659 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: 133
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 24 : Ribosomal protein uL14
DescriptionRibosomal protein uL14
Typepolypeptide(L)
Formula weight14842.553 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: 139
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 25 : Ribosomal protein eL24
DescriptionRibosomal protein eL24
Typepolypeptide(L)
Formula weight17644.857 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: 155
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 26 : Ribosomal protein uL23
DescriptionRibosomal protein uL23
Typepolypeptide(L)
Formula weight18600.809 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: 167
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 27 : Ribosomal protein uL24
DescriptionRibosomal protein uL24
Typepolypeptide(L)
Formula weight16353.228 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: 141
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 28 : Ribosomal protein eL27
DescriptionRibosomal protein eL27
Typepolypeptide(L)
Formula weight16841.355 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: 146
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 29 : Ribosomal protein uL15
DescriptionRibosomal protein uL15
Typepolypeptide(L)
Formula weight16384.355 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: 147
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 30 : Ribosomal protein eL29
DescriptionRibosomal protein eL29
Typepolypeptide(L)
Formula weight6387.679 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: 54
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 31 : Ribosomal protein eL30
DescriptionRibosomal protein eL30
Typepolypeptide(L)
Formula weight11682.658 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: 108
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 32 : Ribosomal protein eL31
DescriptionRibosomal protein eL31
Typepolypeptide(L)
Formula weight14389.729 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: 120
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 33 : Ribosomal protein eL32
DescriptionRibosomal protein eL32
Typepolypeptide(L)
Formula weight15652.334 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: 134
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 34 : Ribosomal protein eL33
DescriptionRibosomal protein eL33
Typepolypeptide(L)
Formula weight12873.091 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: 112
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 35 : Ribosomal protein eL34
DescriptionRibosomal protein eL34
Typepolypeptide(L)
Formula weight15427.309 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: 134
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 36 : Ribosomal protein uL29
DescriptionRibosomal protein uL29
Typepolypeptide(L)
Formula weight14231.108 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: 123
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 37 : Ribosomal protein eL36
DescriptionRibosomal protein eL36
Typepolypeptide(L)
Formula weight11437.687 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: 101
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 38 : Ribosomal protein eL37
DescriptionRibosomal protein eL37
Typepolypeptide(L)
Formula weight11256.210 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: 98
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 39 : Ribosomal protein eL38
DescriptionRibosomal protein eL38
Typepolypeptide(L)
Formula weight9606.386 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: 84
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 40 : Ribosomal protein eL39
DescriptionRibosomal protein eL39
Typepolypeptide(L)
Formula weight6172.519 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:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 41 : Ribosomal protein eL40
DescriptionRibosomal protein eL40
Typepolypeptide(L)
Formula weight14714.291 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: 129
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 42 : Ribosomal protein eL42
DescriptionRibosomal protein eL42
Typepolypeptide(L)
Formula weight12098.689 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: 105
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 43 : Ribosomal protein eL43
DescriptionRibosomal protein eL43
Typepolypeptide(L)
Formula weight10426.384 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: 96
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
LinksSequence view
ID 44 : Ribosomal protein eL28
DescriptionRibosomal protein eL28
Typepolypeptide(L)
Formula weight14787.717 Da
Number of molecules1
ID44
SourceMethod: Isolated from a natural source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 129
NCBI taxonomy: ID:5811
Organism scientific: Toxoplasma gondii
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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44
NameLarge subunit of Toxoplasma gondii 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
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
Processing
3D reconstruction
Image processing id1
Number of particles108162
Resolution3.17 A
Resolution methodFSC 0.143 CUT-OFF
Symmetry typePOINT
Download
PDB format
Allpdb5xxb.ent.gz
pdb5xxb.ent (uncompressed file)
Header onlypdb5xxb.ent.gz
mmCIF format
mmCIF5xxb.cif.gz
XML format
All5xxb.xml.gz
No-atom5xxb-noatom.xml.gz
Ext-atom5xxb-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 6.9 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 7.4 MB