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- PDB-8ova: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RIBOSO... -

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Basic information

Entry
Database: PDB / ID: 8ova
TitleCRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RIBOSOME : PARENTAL STRAIN
Components
  • (40S ribosomal protein ...) x 27
  • (60S ribosomal protein ...) x 34
  • (Ribosomal protein ...) x 7
  • (Ubiquitin-60S ribosomal protein ...) x 2
  • 40S ribosomal proteins S11, putativeRibosome
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • 60S ribosomal subunit protein L31, putative
  • E-SITE TRNA
  • Guanine nucleotide-binding protein subunit beta-like protein
  • LSUa rRNA
  • LSUb rRNA
  • Probable 40S ribosomal protein S9
  • RNA-binding protein
  • SSU rRNA
  • SrRNA-1
  • SrRNA-2
  • SrRNA-4
  • SrRNA-6
  • uS14
KeywordsRIBOSOME / CRYO-EM / TRYPANOSOMA BRUCEI / 80S RIBOSOME
Function / homology
Function and homology information


organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / post-transcriptional regulation of gene expression / phosphate ion binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly ...organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / post-transcriptional regulation of gene expression / phosphate ion binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / RNA processing / 90S preribosome / rescue of stalled ribosome / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / regulation of cytokinesis / positive regulation of apoptotic signaling pathway / regulation of cell growth / small-subunit processome / protein kinase C binding / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / regulation of cell population proliferation / 5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / mRNA binding / apoptotic process / ubiquitin protein ligase binding / nucleolus / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L23 / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal protein S26e signature. ...Ribosomal protein L23 / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal protein S26e signature. / Ribosomal protein S2, eukaryotic / Ribosomal L29e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / : / Ribosomal protein S12e signature. / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S12e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / 40S ribosomal protein S4, C-terminal domain / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S19e / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein L30e, conserved site / Ribosomal protein S23, eukaryotic/archaeal / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal Protein L6, KOW domain / Ribosomal protein L30/YlxQ / Ribosomal protein S25 / S25 ribosomal protein / RS4NT (NUC023) domain / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L14e domain / 60S ribosomal protein L6E / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L34Ae / Ribosomal protein L44e signature. / Ribosomal family S4e / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L19, eukaryotic / Ribosomal protein L7A/L8 / Ribosomal protein L34e / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L6e / Ribosomal protein L14 / Ribosomal protein L30, N-terminal / Ribosomal protein L14, KOW motif / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal L30 N-terminal domain / Ribosomal protein L14 / Ribosomal protein S19A/S15e / Ribosomal protein S8e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S6, eukaryotic / Ribosomal_L40e / Ribosomal protein L40e / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein L40e superfamily
Similarity search - Domain/homology
: / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...: / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL18 / Small ribosomal subunit protein RACK1 / Small ribosomal subunit protein eS12 / 60S ribosomal protein L27, putative / 60S ribosomal protein L18a / RNA-binding protein / 40S ribosomal protein S17, putative / 40S ribosomal protein L14, putative / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL22 / 60S ribosomal protein L29 / Large ribosomal subunit protein eL34 / 40S ribosomal protein S27, putative / 40S ribosomal protein S26 / 40S ribosomal protein S21, putative / 40S ribosomal protein S5, putative / Large ribosomal subunit protein eL28 / 60S ribosomal protein L17, putative / 40S ribosomal protein S4 / Ribosomal protein L37 / 40S ribosomal protein S2, putative / 60S ribosomal protein L6, putative / 40S ribosomal protein S24 / 60S ribosomal protein L37a, putative / 60S ribosomal protein L24, putative / 40S ribosomal protein S10, putative / 40S ribosomal protein S18, putative / Small ribosomal subunit protein eS1 / 60S ribosomal protein L9, putative / 40S ribosomal protein S23, putative / 40S ribosomal proteins S11, putative / 60S ribosomal protein L32, putative / 40S ribosomal protein S6 / Ribosomal protein L36, putative / Ribosomal protein L15 / 60S ribosomal protein L5, putative / 60S ribosomal protein L26, putative / 60S ribosomal subunit protein L31, putative / 60S ribosomal protein L27a / 60S ribosomal protein L23, putative / 60S ribosomal protein L10, putative / 60S ribosomal protein L11, putative / 40S ribosomal protein S3 / 40S ribosomal protein S7 / 60S ribosomal protein L38, putative / 60S ribosomal protein L35, putative / 60S ribosomal protein L21E, putative / 40S ribosomal protein S33, putative / 60S ribosomal protein L39, putative / 60S ribosomal protein L7, putative / 60S ribosomal protein L13 / 60S ribosomal protein L7a / 40S ribosomal protein S16, putative / 60S ribosomal protein L2, putative / Ubiquitin-ribosomal protein eL40 fusion protein / 40S ribosomal protein S15, putative / 40S ribosomal protein S25 / 40S ribosomal protein S8 / 60S ribosomal protein L19, putative / 40S ribosomal protein S15a, putative / Ribosomal protein L3, mitochondrial, putative / 60S ribosomal protein L4 / Ribosomal protein S19, putative / 60S ribosomal protein L35A, putative / 40S ribosomal protein S30 / 60S ribosomal protein L13a, putative / 40S ribosomal protein S13, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsRajan, K.S. / Yonath, A.
Funding supportEuropean Union, Israel, 2items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Israel Science Foundation Israel
CitationJournal: Nat Commun / Year: 2023
Title: A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei.
Authors: K Shanmugha Rajan / Hava Madmoni / Anat Bashan / Masato Taoka / Saurav Aryal / Yuko Nobe / Tirza Doniger / Beathrice Galili Kostin / Amit Blumberg / Smadar Cohen-Chalamish / Schraga Schwartz ...Authors: K Shanmugha Rajan / Hava Madmoni / Anat Bashan / Masato Taoka / Saurav Aryal / Yuko Nobe / Tirza Doniger / Beathrice Galili Kostin / Amit Blumberg / Smadar Cohen-Chalamish / Schraga Schwartz / Andre Rivalta / Ella Zimmerman / Ron Unger / Toshiaki Isobe / Ada Yonath / Shulamit Michaeli /
Abstract: Trypanosomes are protozoan parasites that cycle between insect and mammalian hosts and are the causative agent of sleeping sickness. Here, we describe the changes of pseudouridine (Ψ) modification ...Trypanosomes are protozoan parasites that cycle between insect and mammalian hosts and are the causative agent of sleeping sickness. Here, we describe the changes of pseudouridine (Ψ) modification on rRNA in the two life stages of the parasite using four different genome-wide approaches. CRISPR-Cas9 knock-outs of all four snoRNAs guiding Ψ on helix 69 (H69) of the large rRNA subunit were lethal. A single knock-out of a snoRNA guiding Ψ530 on H69 altered the composition of the 80S monosome. These changes specifically affected the translation of only a subset of proteins. This study correlates a single site Ψ modification with changes in ribosomal protein stoichiometry, supported by a high-resolution cryo-EM structure. We propose that alteration in rRNA modifications could generate ribosomes preferentially translating state-beneficial proteins.
History
DepositionApr 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
BA: LSUa rRNA
AA: SSU rRNA
BB: LSUb rRNA
BH: SrRNA-4
BG: SrRNA-2
BF: SrRNA-6
BE: SrRNA-1
BD: 5S rRNA
BC: 5.8S rRNA
AB: E-SITE TRNA
AQ: Ribosomal protein S10
A8: uS14
A9: Ubiquitin-60S ribosomal protein L40
Az: RNA-binding protein
AH: 40S ribosomal protein S14
AI: 40S ribosomal protein S15, putative
AJ: 40S ribosomal protein S15a, putative
AK: 40S ribosomal protein S16, putative
AM: 40S ribosomal protein S18, putative
AO: Ribosomal protein S19, putative
AP: 40S ribosomal protein S2, putative
AR: 40S ribosomal protein S21, putative
AS: 40S ribosomal protein S23, putative
AT: 40S ribosomal protein S24
AU: 40S ribosomal protein S25
AV: 40S ribosomal protein S26
AW: 40S ribosomal protein S27, putative
AX: 40S ribosomal protein S3, putative
AY: 40S ribosomal protein S30
AZ: 40S ribosomal protein S33, putative
AL: 40S ribosomal protein S17, putative
A0: 40S ribosomal protein S3a
A1: 40S ribosomal protein S4
A2: 40S ribosomal protein S5, putative
A3: 40S ribosomal protein S6
A4: 40S ribosomal protein S7
A5: 40S ribosomal protein S8
A6: Probable 40S ribosomal protein S9
A7: Guanine nucleotide-binding protein subunit beta-like protein
AC: 40S ribosomal protein SA
AD: 40S ribosomal protein S10, putative
AE: 40S ribosomal proteins S11, putative
AG: 40S ribosomal protein S13, putative
Bh: 60S ribosomal subunit protein L31, putative
Ba: 60S ribosomal protein L27
Bb: 60S ribosomal protein L27a
Bc: 60S ribosomal protein L28, putative
Bd: 60S ribosomal protein L29
Be: 60S ribosomal protein L2, putative
Bz: Ribosomal protein L41
Bg: 60S ribosomal protein L30
Bf: Ribosomal protein L3, mitochondrial, putative
BI: 60S ribosomal protein L18
Bj: 60S ribosomal protein L34, putative
BK: 60S ribosomal protein L10, putative
Bk: 60S ribosomal protein L35, putative
BL: 60S ribosomal protein L11, putative
Bl: 60S ribosomal protein L35A, putative
Bm: Ribosomal protein L36, putative
BN: 60S ribosomal protein L13
Bn: Ribosomal protein L37
BO: 60S ribosomal protein L13a, putative
Bo: 60S ribosomal protein L37a, putative
Bp: 60S ribosomal protein L38, putative
Bq: 60S ribosomal protein L39, putative
BQ: Ribosomal protein L15
BR: 60S ribosomal protein L17, putative
Br: 60S ribosomal protein L4
BS: 60S ribosomal protein L18a
Bs: Ubiquitin-60S ribosomal protein L40
BT: 60S ribosomal protein L19, putative
Bt: 60S ribosomal protein L44
BU: 60S ribosomal protein L21E, putative
Bu: 60S ribosomal protein L5, putative
BV: 60S ribosomal protein L22, putative
Bv: 60S ribosomal protein L6, putative
BW: 60S ribosomal protein L23, putative
BX: 60S ribosomal protein L23a
Bw: 60S ribosomal protein L7, putative
Bx: 60S ribosomal protein L7a
BY: 60S ribosomal protein L24, putative
By: 60S ribosomal protein L9, putative
BZ: 60S ribosomal protein L26, putative
Bi: 60S ribosomal protein L32, putative
BP: 40S ribosomal protein L14, putative
AF: 40S ribosomal protein S12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,661,531411
Polymers3,652,82586
Non-polymers8,706325
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 10 types, 10 molecules BAAABBBHBGBFBEBDBCAB

#1: RNA chain LSUa rRNA


Mass: 619662.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#2: RNA chain SSU rRNA


Mass: 734961.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#3: RNA chain LSUb rRNA / LSU_beta rRNA


Mass: 494694.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#4: RNA chain SrRNA-4


Mass: 43694.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 10519
#5: RNA chain SrRNA-2


Mass: 59196.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 10528
#6: RNA chain SrRNA-6


Mass: 24646.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 62359081
#7: RNA chain SrRNA-1


Mass: 69132.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 10528
#8: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38316.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 162230
#9: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 67019.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 10527
#10: RNA chain E-SITE TRNA


Mass: 6106.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)

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Ribosomal protein ... , 7 types, 7 molecules AQAOBzBfBmBnBQ

#11: Protein Ribosomal protein S10 / / uS10


Mass: 13377.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#20: Protein Ribosomal protein S19, putative / Ribosome


Mass: 18891.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q583K7
#50: Protein/peptide Ribosomal protein L41 / / eL41


Mass: 4348.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#52: Protein Ribosomal protein L3, mitochondrial, putative / Ribosome


Mass: 48802.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q581Q1
#59: Protein Ribosomal protein L36, putative / Ribosome


Mass: 12491.966 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CY6
#61: Protein Ribosomal protein L37 /


Mass: 10128.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q386L1
#66: Protein Ribosomal protein L15 /


Mass: 26461.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CY7

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Protein , 6 types, 6 molecules A8AzA6A7AEBh

#12: Protein uS14


Mass: 6744.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#14: Protein RNA-binding protein /


Mass: 30340.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q382D5
#38: Protein Probable 40S ribosomal protein S9


Mass: 22098.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P17959
#39: Protein Guanine nucleotide-binding protein subunit beta-like protein / Activated protein kinase C receptor homolog


Mass: 34727.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P69103
#42: Protein 40S ribosomal proteins S11, putative / Ribosome


Mass: 20132.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CI4
#44: Protein 60S ribosomal subunit protein L31, putative /


Mass: 21752.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38DH8

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Ubiquitin-60S ribosomal protein ... , 2 types, 2 molecules A9Bs

#13: Protein Ubiquitin-60S ribosomal protein L40


Mass: 16936.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57WI3
#70: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14685.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P21899

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40S ribosomal protein ... , 27 types, 27 molecules AHAIAJAKAMAPARASATAUAVAWAXAYAZALA0A1A2A3A4A5ACADAGBPAF

#15: Protein 40S ribosomal protein S14 /


Mass: 15540.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P19800
#16: Protein 40S ribosomal protein S15, putative / Ribosome


Mass: 17512.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57XN7
#17: Protein 40S ribosomal protein S15a, putative / Ribosome


Mass: 14669.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q580K6
#18: Protein 40S ribosomal protein S16, putative / Ribosome


Mass: 17031.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57VV0
#19: Protein 40S ribosomal protein S18, putative / Ribosome


Mass: 17548.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38B69
#21: Protein 40S ribosomal protein S2, putative / Ribosome


Mass: 28688.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q388D3
#22: Protein 40S ribosomal protein S21, putative / Ribosome


Mass: 21156.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q385B8
#23: Protein 40S ribosomal protein S23, putative / Ribosome


Mass: 15963.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CD1
#24: Protein 40S ribosomal protein S24 /


Mass: 15722.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38AM9
#25: Protein 40S ribosomal protein S25 /


Mass: 12589.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57XX0
#26: Protein 40S ribosomal protein S26 /


Mass: 12837.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q384J9
#27: Protein 40S ribosomal protein S27, putative / Ribosome


Mass: 9648.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383V7
#28: Protein 40S ribosomal protein S3, putative / Ribosome


Mass: 24259.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38EW1
#29: Protein 40S ribosomal protein S30 /


Mass: 7454.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q584U5
#30: Protein 40S ribosomal protein S33, putative / Ribosome


Mass: 11186.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57U30
#31: Protein 40S ribosomal protein S17, putative / Ribosome


Mass: 16259.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q382Z8
#32: Protein 40S ribosomal protein S3a /


Mass: 29477.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38BK6
#33: Protein 40S ribosomal protein S4 /


Mass: 30704.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q386F2
#34: Protein 40S ribosomal protein S5, putative / Ribosome


Mass: 21424.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q385D9
#35: Protein 40S ribosomal protein S6 /


Mass: 28507.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CL9
#36: Protein 40S ribosomal protein S7 /


Mass: 23889.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38FD9
#37: Protein 40S ribosomal protein S8 /


Mass: 25001.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57YL6
#40: Protein 40S ribosomal protein SA /


Mass: 31395.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383I8
#41: Protein 40S ribosomal protein S10, putative / Ribosome


Mass: 19322.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38B66
#43: Protein 40S ribosomal protein S13, putative / Ribosome


Mass: 17347.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q586C2
#85: Protein 40S ribosomal protein L14, putative / Ribosome


Mass: 21521.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383F5
#86: Protein 40S ribosomal protein S12 /


Mass: 15889.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q03253

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60S ribosomal protein ... , 34 types, 34 molecules BaBbBcBdBeBgBIBjBKBkBLBlBNBOBoBpBqBRBrBSBTBtBUBuBVBvBWBXBwBx...

#45: Protein 60S ribosomal protein L27 /


Mass: 15618.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q381J6
#46: Protein 60S ribosomal protein L27a /


Mass: 16307.155 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38DN9
#47: Protein 60S ribosomal protein L28, putative / Ribosome


Mass: 16901.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q385E9
#48: Protein 60S ribosomal protein L29 /


Mass: 8244.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383S6
#49: Protein 60S ribosomal protein L2, putative / Ribosome


Mass: 28372.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57W56
#51: Protein 60S ribosomal protein L30 /


Mass: 11531.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P49153
#53: Protein 60S ribosomal protein L18 /


Mass: 21929.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P50885
#54: Protein 60S ribosomal protein L34, putative / Ribosome


Mass: 19396.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383V6
#55: Protein 60S ribosomal protein L10, putative / Ribosome


Mass: 24785.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38EC5
#56: Protein 60S ribosomal protein L35, putative / Ribosome


Mass: 15187.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38FW8
#57: Protein 60S ribosomal protein L11, putative / Ribosome


Mass: 22420.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38EI9
#58: Protein 60S ribosomal protein L35A, putative / Ribosome


Mass: 17061.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q584G9
#60: Protein 60S ribosomal protein L13 /


Mass: 25491.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57V55
#62: Protein 60S ribosomal protein L13a, putative / Ribosome


Mass: 25775.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q585J5
#63: Protein 60S ribosomal protein L37a, putative / Ribosome


Mass: 10482.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38AW9
#64: Protein 60S ribosomal protein L38, putative / Ribosome


Mass: 9527.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38FV6
#65: Protein 60S ribosomal protein L39, putative / Ribosome


Mass: 6567.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57UJ8
#67: Protein 60S ribosomal protein L17, putative / Ribosome


Mass: 19147.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q385T6
#68: Protein 60S ribosomal protein L4 /


Mass: 41941.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q582N2
#69: Protein 60S ribosomal protein L18a /


Mass: 20950.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q382C4
#71: Protein 60S ribosomal protein L19, putative / Ribosome


Mass: 29494.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57ZI7
#72: Protein 60S ribosomal protein L44 /


Mass: 12488.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P17843
#73: Protein 60S ribosomal protein L21E, putative / Ribosome


Mass: 18043.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q4FKD4
#74: Protein 60S ribosomal protein L5, putative / Ribosome


Mass: 34710.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CY8
#75: Protein 60S ribosomal protein L22, putative / Ribosome


Mass: 15288.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383R3
#76: Protein 60S ribosomal protein L6, putative / Ribosome


Mass: 21232.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q389K1
#77: Protein 60S ribosomal protein L23, putative / Ribosome


Mass: 14989.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38DP2
#78: Protein 60S ribosomal protein L23a / / L25


Mass: 18211.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P41165
#79: Protein 60S ribosomal protein L7, putative / Ribosome


Mass: 29416.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57V35
#80: Protein 60S ribosomal protein L7a /


Mass: 30945.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57VM1
#81: Protein 60S ribosomal protein L24, putative / Ribosome


Mass: 14633.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38B56
#82: Protein 60S ribosomal protein L9, putative / Ribosome


Mass: 21897.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CD0
#83: Protein 60S ribosomal protein L26, putative / Ribosome


Mass: 16497.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38D25
#84: Protein 60S ribosomal protein L32, putative / Ribosome


Mass: 15432.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CL1

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Non-polymers , 5 types, 514 molecules

#87: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 234 / Source method: obtained synthetically / Formula: Mg
#88: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: K
#89: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Na
#90: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#91: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RIBOSOME : PARENTAL STRAIN
Type: RIBOSOME / Entity ID: #1-#86 / Source: NATURAL
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 1.17 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459985 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004224091
ELECTRON MICROSCOPYf_angle_d0.606328896
ELECTRON MICROSCOPYf_dihedral_angle_d17.19777892
ELECTRON MICROSCOPYf_chiral_restr0.03840957
ELECTRON MICROSCOPYf_plane_restr0.00421356

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