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

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Basic information

Entry
Database: PDB / ID: 8ove
TitleCRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RIBOSOME : TB11CS6H1 snoRNA mutant
Components
  • (40S ribosomal protein ...) x 26
  • (60S ribosomal protein ...) x 33
  • (Ribosomal protein ...) x 8
  • 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
  • HIS-THR-CYS-THR
  • LSUb rRNA
  • LUS_alpha rRNA
  • Probable 40S ribosomal protein S9
  • Putative ribosomal protein S29
  • RNA-binding protein
  • SSU rRNA
  • SrRNA 1
  • SrRNA 2
  • SrRNA 4
  • SrRNA 6
  • Ubiquitin-60S ribosomal protein L40
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 / 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 / translation regulator activity ...organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / 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 / translation regulator activity / 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) / RNA processing / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA / ribosome assembly / small-subunit processome / regulation of cytokinesis / regulation of cell growth / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / small ribosomal subunit / cytoplasmic translation / regulation of cell population proliferation / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / apoptotic process / nucleolus / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein L29e / Ribosomal protein S26e ...Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein L29e / Ribosomal protein S26e / Ribosomal protein S26e signature. / Ribosomal protein S25 / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / Ribosomal L29e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / S25 ribosomal protein / Ribosomal protein S19A/S15e / Ribosomal protein S30 / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8e, conserved site / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal S17 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L38e protein family / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L22e protein family / Ribosomal protein S17, archaeal/eukaryotic / 40S Ribosomal protein S10 / 60S ribosomal protein L35 / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S3Ae / Plectin/S10, N-terminal / Ribosomal S3Ae family / Ribosomal protein S7e / Ribosomal L27e protein family / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein L30/YlxQ / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L34e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L37ae / RS4NT (NUC023) domain / Ribosomal protein L14e domain / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L6E / Ribosomal protein S27 / Ribosomal L40e family / Ribosomal S3Ae family / Ribosomal protein L35A / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e
Similarity search - Domain/homology
: / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...: / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L24 / 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 / 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 / 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 / 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: 2.6 Å
AuthorsRajan, K.S. / Yonath, A.
Funding support Israel, European Union, 2items
OrganizationGrant numberCountry
Israel Science Foundation Israel
European Research Council (ERC)European Union
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
AA: SSU rRNA
AB: E-SITE TRNA
BA: LUS_alpha rRNA
BB: LSUb rRNA
BC: 5.8S rRNA
BD: 5S rRNA
BE: SrRNA 1
BP: 40S ribosomal protein L14, putative
BQ: Ribosomal protein L15
BR: 60S ribosomal protein L17, putative
BS: 60S ribosomal protein L18a
BT: 60S ribosomal protein L19, putative
BU: 60S ribosomal protein L21E, putative
BW: 60S ribosomal protein L23, putative
BY: Ribosomal protein L24
BX: 60S ribosomal protein L23a
BZ: 60S ribosomal protein L26, putative
Bp: 60S ribosomal protein L38, putative
Bq: 60S ribosomal protein L39, putative
Br: 60S ribosomal protein L4
Bt: 60S ribosomal protein L44
Bw: 60S ribosomal protein L7, putative
Bx: 60S ribosomal protein L7a
Bl: 60S ribosomal protein L35A, putative
Bu: 60S ribosomal protein L5, putative
By: 60S ribosomal protein L9, putative
A0: 40S ribosomal protein S3a
A2: 40S ribosomal protein S5, putative
A5: 40S ribosomal protein S8
AD: 40S ribosomal protein S10, putative
A8: Putative ribosomal protein S29
AE: 40S ribosomal proteins S11, putative
AG: 40S ribosomal protein S13, putative
AI: 40S ribosomal protein S15, putative
AH: 40S ribosomal protein S14
AJ: 40S ribosomal protein S15a, putative
AL: 40S ribosomal protein S17, putative
AM: 40S ribosomal protein S18, putative
AO: Ribosomal protein S19, putative
AP: 40S ribosomal protein S2, putative
AS: 40S ribosomal protein S23, putative
AU: 40S ribosomal protein S25
AX: 40S ribosomal protein S3, putative
AZ: 40S ribosomal protein S33, putative
A3: 40S ribosomal protein S6
AT: 40S ribosomal protein S24
A1: 40S ribosomal protein S4
AC: 40S ribosomal protein SA
Bc: 60S ribosomal protein L28, putative
Bz: Ribosomal protein L41
Bo: 60S ribosomal protein L37a, putative
Bn: Ribosomal protein L37
Bm: Ribosomal protein L36, putative
Bk: 60S ribosomal protein L35, putative
Bj: 60S ribosomal protein L34, putative
Bi: 60S ribosomal protein L32, putative
Bg: 60S ribosomal protein L30
Bd: 60S ribosomal protein L29
Bb: 60S ribosomal protein L27a
Ba: 60S ribosomal protein L27
BO: 60S ribosomal protein L13a, putative
BN: 60S ribosomal protein L13
BL: 60S ribosomal protein L11, putative
BK: 60S ribosomal protein L10, putative
BI: 60S ribosomal protein L18
Be: 60S ribosomal protein L2, putative
AK: 40S ribosomal protein S16, putative
A6: Probable 40S ribosomal protein S9
Bf: Ribosomal protein L3, mitochondrial, putative
AY: 40S ribosomal protein S30
Bv: 60S ribosomal protein L6, putative
Bh: 60S ribosomal subunit protein L31, putative
BF: SrRNA 6
BG: SrRNA 2
BH: SrRNA 4
Bs: Ubiquitin-60S ribosomal protein L40
BV: 60S ribosomal protein L22, putative
Az: RNA-binding protein
AQ: Ribosomal protein S10
AR: 40S ribosomal protein S21, putative
AV: 40S ribosomal protein S26
AW: 40S ribosomal protein S27, putative
A4: 40S ribosomal protein S7
A7: Guanine nucleotide-binding protein subunit beta-like protein
A: HIS-THR-CYS-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,626,290326
Polymers3,619,89385
Non-polymers6,397241
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 10 types, 10 molecules AAABBABBBCBDBEBFBGBH

#1: RNA chain SSU rRNA


Mass: 734333.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#2: 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)
#3: RNA chain LUS_alpha rRNA


Mass: 619662.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#4: 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)
#5: 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
#6: 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
#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
#73: 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
#74: 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
#75: 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

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40S ribosomal protein ... , 26 types, 26 molecules BPA0A2A5ADAGAIAHAJALAMAPASAUAXAZA3ATA1ACAKAYARAVAWA4

#8: 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
#27: 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
#28: 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
#29: 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
#30: 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
#33: 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
#34: 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
#35: 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
#36: 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
#37: 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
#38: 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
#40: 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
#41: 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
#42: 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
#43: 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
#44: 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
#45: 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
#46: 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
#47: 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
#48: 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
#67: 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
#70: 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
#80: Protein 40S ribosomal protein S21, putative / Ribosome


Mass: 21228.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q385B8
#81: 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
#82: 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
#83: 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

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Ribosomal protein ... , 8 types, 8 molecules BQBYAOBzBnBmBfAQ

#9: 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
#15: Protein Ribosomal protein L24 /


Mass: 14633.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: O77067
#39: 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 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
#53: 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
#69: 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
#79: 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)

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60S ribosomal protein ... , 33 types, 33 molecules BRBSBTBUBWBXBZBpBqBrBtBwBxBlBuByBcBoBkBjBiBgBdBbBaBOBNBLBKBI...

#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#49: 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
#51: 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
#54: 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
#55: 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
#56: 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
#57: 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
#58: 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
#59: 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
#60: 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
#61: 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
#62: 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
#63: 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
#64: 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
#65: 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
#66: 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
#71: 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 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

-
Protein , 7 types, 7 molecules A8AEA6BhBsAzA7

#31: Protein Putative ribosomal protein S29 /


Mass: 6744.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#32: 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
#68: 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
#72: 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
#76: 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
#78: 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
#84: Protein Guanine nucleotide-binding protein subunit beta-like protein / Activated protein kinase C receptor homolog


Mass: 34715.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P69103

-
Protein/peptide , 1 types, 1 molecules A

#85: Protein/peptide HIS-THR-CYS-THR


Mass: 461.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Production host: Trypanosoma brucei brucei (eukaryote)

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Non-polymers , 4 types, 564 molecules

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


Mass: 24.305 Da / Num. of mol.: 149 / Source method: obtained synthetically / Formula: Mg
#87: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: K
#88: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: Na
#89: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 80S ribosomeEukaryotic ribosome / Type: RIBOSOME / Entity ID: #1-#17, #19-#37, #39-#85 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
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: 1.16 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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 552813 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
14V8M

4v8m

14V8M1PDBexperimental model
28A3W

8a3w

18A3W2PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004217787
ELECTRON MICROSCOPYf_angle_d0.634319685
ELECTRON MICROSCOPYf_dihedral_angle_d17.36175708
ELECTRON MICROSCOPYf_chiral_restr0.03939817
ELECTRON MICROSCOPYf_plane_restr0.00520677

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