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- PDB-9sul: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI BLOODSTREAM FORM 80S RIBOSOME -

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Basic information

Entry
Database: PDB / ID: 9sul
TitleCRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI BLOODSTREAM FORM 80S RIBOSOME
Components
  • (40S ribosomal protein ...) x 25
  • (60S ribosomal protein ...) x 34
  • (Ribosomal protein ...) x 6
  • (Small ribosomal subunit protein ...) x 4
  • (Ubiquitin-60S ribosomal protein ...) x 2
  • 40S ribosomal proteins S11, putative
  • 5.8S rRNA
  • 5S rRNA
  • 60S ribosomal subunit protein L31, putative
  • E-SITE TRNA
  • LSUa rRNA
  • LSUb rRNA
  • Probable 40S ribosomal protein S9
  • Putative ribosomal protein S29
  • RNA-binding protein
  • SSU rRNA
  • SrRNA-1
  • SrRNA-2
  • SrRNA-4
  • SrRNA-6
KeywordsRIBOSOME / CRYO-EM / TRYPANOSOMA BRUCEI / BLOODSTREAM FORM / 80S
Function / homology
Function and homology information


organellar small ribosomal subunit / organellar large ribosomal subunit / kinetoplast / nuclear lumen / ciliary plasm / ciliary transition zone / mitochondrial large ribosomal subunit / post-transcriptional regulation of gene expression / phosphate ion binding / RNA processing ...organellar small ribosomal subunit / organellar large ribosomal subunit / kinetoplast / nuclear lumen / ciliary plasm / ciliary transition zone / mitochondrial large ribosomal subunit / post-transcriptional regulation of gene expression / phosphate ion binding / RNA processing / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / 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 / regulation of cytokinesis / ribosome assembly / ribosomal large subunit biogenesis / 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 / regulation of cell growth / small-subunit processome / modification-dependent protein catabolic process / ribosome biogenesis / protein tag activity / rRNA processing / cytosolic ribosome / ribosomal small subunit assembly / regulation of cell population proliferation / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / protein ubiquitination / apoptotic process / ribonucleoprotein complex / structural constituent of ribosome / ribosome / translation / mRNA binding / nucleolus / mitochondrion / metal ion binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L14, KOW motif / : / : / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / : / Ribosomal protein S26e signature. ...Ribosomal protein L14, KOW motif / : / : / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L13e / Ribosomal L38e protein family / Ribosomal protein S21e / Ribosomal protein L38e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Plectin/S10, N-terminal / Ribosomal protein L18/L18-A/B/e, conserved site / Plectin/S10 domain / Ribosomal protein L18e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal L40e family / Ribosomal protein S25 / S25 ribosomal protein / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / : / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L44e / Ribosomal protein L44 / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L7A/L8 / 60S ribosomal protein L35 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L6e / Ribosomal protein L30e signature 2. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L30e, conserved site / 60S ribosomal protein L6E / Ribosomal protein L7, eukaryotic / : / Ribosomal protein L30, N-terminal / Ribosomal protein L39e, conserved site / Ribosomal L30 N-terminal domain / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein S8e, conserved site / Ribosomal protein L34e / Ribosomal protein S8e signature. / 60S ribosomal protein L19 / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus
Similarity search - Domain/homology
GENETICIN / GUANOSINE-5'-TRIPHOSPHATE / : / 1,4-DIAMINOBUTANE / SPERMIDINE / : / : / : / : / : ...GENETICIN / GUANOSINE-5'-TRIPHOSPHATE / : / 1,4-DIAMINOBUTANE / SPERMIDINE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS10 / 60S ribosomal protein L41 / Putative ribosomal protein S29 / 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 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL27 / 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 / 60S ribosomal protein L34, putative / 40S ribosomal protein S27, putative / 40S ribosomal protein S26 / 40S ribosomal protein S21, putative / 40S ribosomal protein S5, putative / 60S ribosomal protein L28, putative / 60S ribosomal protein L17, putative / 40S ribosomal protein S4 / Ribosomal protein L37 / Small ribosomal subunit protein uS5 / 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 / Large ribosomal subunit protein uL5 / 40S ribosomal protein S3 / 40S ribosomal protein S7 / Large ribosomal subunit protein eL38 / 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: 2.1 Å
AuthorsRajan, K.S. / Yonath, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation Israel
CitationJournal: To Be Published
Title: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI BLOODSTREAM FORM 80S RIBOSOME
Authors: Rajan, K.S. / Yonath, A.
History
DepositionSep 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Et: E-SITE TRNA
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: Small ribosomal subunit protein RACK1
A8: Putative ribosomal protein S29
A9: Ubiquitin-60S ribosomal protein L40
AA: SSU rRNA
AC: 40S ribosomal protein SA
AD: 40S ribosomal protein S10, putative
AE: 40S ribosomal proteins S11, putative
AF: Small ribosomal subunit protein eS12
AG: 40S ribosomal protein S13, putative
AH: Small ribosomal subunit protein uS11
AI: 40S ribosomal protein S15, putative
AJ: 40S ribosomal protein S15a, putative
AK: 40S ribosomal protein S16, putative
AL: 40S ribosomal protein S17, putative
AM: 40S ribosomal protein S18, putative
AO: Ribosomal protein S19, putative
AP: 40S ribosomal protein S2, putative
AQ: Small ribosomal subunit protein uS10
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
Az: RNA-binding protein
BA: LSUa rRNA
BB: LSUb rRNA
BC: 5.8S rRNA
BD: 5S rRNA
BE: SrRNA-1
BF: SrRNA-6
BG: SrRNA-2
BH: SrRNA-4
BI: 60S ribosomal protein L18
BK: 60S ribosomal protein L10, putative
BL: 60S ribosomal protein L11, putative
BN: 60S ribosomal protein L13
BO: 60S ribosomal protein L13a, putative
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
BV: 60S ribosomal protein L22, putative
BW: 60S ribosomal protein L23, putative
BX: 60S ribosomal protein L23a
BY: Ribosomal protein L24
BZ: 60S ribosomal protein L26, 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
Bf: Ribosomal protein L3, mitochondrial, putative
Bg: 60S ribosomal protein L30
Bh: 60S ribosomal subunit protein L31, putative
Bi: 60S ribosomal protein L32, putative
Bj: 60S ribosomal protein L34, putative
Bk: 60S ribosomal protein L35, putative
Bl: 60S ribosomal protein L35A, putative
Bm: Ribosomal protein L36, putative
Bn: Ribosomal protein L37
Bo: 60S ribosomal protein L37a, putative
Bp: 60S ribosomal protein L38, putative
Bq: 60S ribosomal protein L39, putative
Br: 60S ribosomal protein L4
Bs: Ubiquitin-60S ribosomal protein L40
Bt: 60S ribosomal protein L44
Bu: 60S ribosomal protein L5, putative
Bv: 60S ribosomal protein L6, putative
Bw: 60S ribosomal protein L7, putative
Bx: 60S ribosomal protein L7a
By: 60S ribosomal protein L9, putative
Bz: 60S ribosomal protein L41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,684,275482
Polymers3,663,09786
Non-polymers21,178396
Water49,5052748
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 10 types, 10 molecules EtAABABBBCBDBEBFBGBH

#1: RNA chain E-SITE TRNA


Mass: 30637.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#12: RNA chain SSU rRNA


Mass: 734203.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#37: RNA chain LSUa rRNA


Mass: 602633.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#38: RNA chain LSUb rRNA


Mass: 497231.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#39: RNA chain 5.8S rRNA


Mass: 67019.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 10527
#40: RNA chain 5S rRNA


Mass: 38621.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 162230
#41: RNA chain SrRNA-1


Mass: 69461.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 10528
#42: 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
#43: 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
#44: 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 ... , 25 types, 25 molecules A0A1A2A3A4A5ACADAGAIAJAKALAMAPARASATAUAVAWAXAYAZBP

#2: 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
#3: 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
#4: Protein 40S ribosomal protein S5, putative


Mass: 21424.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q385D9
#5: 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
#6: Protein 40S ribosomal protein S7


Mass: 23934.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38FD9
#7: 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
#13: 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
#14: Protein 40S ribosomal protein S10, putative


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


Mass: 17347.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q586C2
#19: Protein 40S ribosomal protein S15, putative


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


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


Mass: 17047.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57VV0
#22: Protein 40S ribosomal protein S17, putative


Mass: 16259.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q382Z8
#23: Protein 40S ribosomal protein S18, putative


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


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


Mass: 21185.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q385B8
#28: Protein 40S ribosomal protein S23, putative


Mass: 15979.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CD1
#29: 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
#30: 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
#31: 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
#32: Protein 40S ribosomal protein S27, putative


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


Mass: 24259.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38EW1
#34: 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
#35: Protein 40S ribosomal protein S33, putative


Mass: 11186.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57U30
#50: Protein 40S ribosomal protein L14, putative


Mass: 21521.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383F5

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Protein , 5 types, 5 molecules A6A8AEAzBh

#8: 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
#10: 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) / References: UniProt: G0UD55
#15: Protein 40S ribosomal proteins S11, putative


Mass: 20132.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CI4
#36: 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
#68: 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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Small ribosomal subunit protein ... , 4 types, 4 molecules A7AFAHAQ

#9: Protein Small ribosomal subunit protein RACK1 / Activated protein kinase C receptor homolog / Guanine nucleotide-binding protein subunit beta-like protein


Mass: 34756.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P69103
#16: Protein Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


Mass: 15918.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q03253
#18: Protein Small ribosomal subunit protein uS11 / 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
#26: Protein Small ribosomal subunit protein uS10


Mass: 13377.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6KWF3

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

#11: 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
#79: 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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Ribosomal protein ... , 6 types, 6 molecules AOBQBYBfBmBn

#24: Protein Ribosomal protein S19, putative


Mass: 18891.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q583K7
#51: Protein Ribosomal protein L15


Mass: 26477.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CY7
#59: 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
#66: Protein Ribosomal protein L3, mitochondrial, putative


Mass: 48816.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q581Q1
#73: Protein Ribosomal protein L36, putative


Mass: 12491.966 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CY6
#74: 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

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

#45: 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
#46: Protein 60S ribosomal protein L10, putative


Mass: 24785.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38EC5
#47: Protein 60S ribosomal protein L11, putative


Mass: 22420.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38EI9
#48: 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
#49: Protein 60S ribosomal protein L13a, putative


Mass: 25791.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q585J5
#52: Protein 60S ribosomal protein L17, putative


Mass: 19147.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q385T6
#53: Protein 60S ribosomal protein L18a


Mass: 21008.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q382C4
#54: Protein 60S ribosomal protein L19, putative


Mass: 29494.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57ZI7
#55: Protein 60S ribosomal protein L21E, putative / Ribosomal protein L21E (60S) / putative


Mass: 18072.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q4FKD4
#56: Protein 60S ribosomal protein L22, putative


Mass: 15288.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383R3
#57: Protein 60S ribosomal protein L23, putative


Mass: 14989.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38DP2
#58: 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
#60: Protein 60S ribosomal protein L26, putative


Mass: 16497.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38D25
#61: 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
#62: 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
#63: Protein 60S ribosomal protein L28, putative


Mass: 16901.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q385E9
#64: 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
#65: Protein 60S ribosomal protein L2, putative


Mass: 28401.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57W56
#67: 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
#69: Protein 60S ribosomal protein L32, putative


Mass: 15432.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CL1
#70: Protein 60S ribosomal protein L34, putative


Mass: 19396.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383V6
#71: Protein 60S ribosomal protein L35, putative


Mass: 15187.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38FW8
#72: Protein 60S ribosomal protein L35A, putative


Mass: 17061.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q584G9
#75: Protein 60S ribosomal protein L37a, putative


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


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


Mass: 6567.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57UJ8
#78: 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
#80: 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
#81: Protein 60S ribosomal protein L5, putative


Mass: 34710.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CY8
#82: Protein 60S ribosomal protein L6, putative


Mass: 21248.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q389K1
#83: Protein 60S ribosomal protein L7, putative


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


Mass: 30961.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57VM1
#85: Protein 60S ribosomal protein L9, putative


Mass: 21897.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CD0
#86: Protein/peptide 60S ribosomal protein L41


Mass: 4348.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: G0U1J3

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Non-polymers , 9 types, 3144 molecules

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


Mass: 24.305 Da / Num. of mol.: 224 / Source method: obtained synthetically / Formula: Mg
#88: Chemical...
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 62 / Source method: obtained synthetically / Formula: C7H19N3
#89: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#90: Chemical ChemComp-GET / GENETICIN / G418


Mass: 496.552 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H40N4O10 / Comment: antibiotic*YM
#91: Chemical
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C4H12N2
#92: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#93: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 69 / Source method: obtained synthetically / Formula: K
#94: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Na
#95: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2748 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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 BLOODSTREAM FORM 80S RIBOSOME
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 1.05 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX1.21.2_5419model refinement
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 570752 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 28.1 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036223614
ELECTRON MICROSCOPYf_angle_d0.685327490
ELECTRON MICROSCOPYf_chiral_restr0.039740651
ELECTRON MICROSCOPYf_plane_restr0.006421438
ELECTRON MICROSCOPYf_dihedral_angle_d22.516491618

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