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- PDB-9yxb: Babesia divergens ribosome structure by single-particle cryo-EM (... -

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Entry
Database: PDB / ID: 9yxb
TitleBabesia divergens ribosome structure by single-particle cryo-EM (3D class1, A-, P-, and E-site tRNAs and mRNA)
Components
  • (40S ribosomal protein ...) x 32
  • (60S ribosomal protein ...) x 41
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • A-site tRNA
  • E-site tRNA
  • P-site tRNA
  • Receptor for activated C kinase 1, RACK1 protein
  • mRNA fragment
KeywordsRIBOSOME / tRNAs / RNA modification / 80S
Function / homology
Function and homology information


preribosome / 90S preribosome / protein-RNA complex assembly / translation regulator activity / 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 / small-subunit processome / chloroplast ...preribosome / 90S preribosome / protein-RNA complex assembly / translation regulator activity / 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 / small-subunit processome / chloroplast / kinase activity / rRNA processing / large ribosomal subunit / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / translation / structural constituent of ribosome / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / : / Ribosomal protein S26e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L29e ...: / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / : / Ribosomal protein S26e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L19/L19e conserved site / Plectin/S10 domain / Ribosomal protein L19e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal L40e family / Ribosomal protein S10, eukaryotic/archaeal / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / : / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein 60S L18 and 50S L18e / 60S ribosomal protein L35 / Ribosomal protein L6e / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L7A/L8 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L30e signature 2. / 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. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / 60S ribosomal protein L19 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L36e / Ribosomal protein L14e domain / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein S14p/S29e / Ribosomal protein S27a family protein / Ribosomal protein L24 family protein ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein S14p/S29e / Ribosomal protein S27a family protein / Ribosomal protein L24 family protein / Plectin/S10 domain containing protein / 40S ribosomal protein S12 / 60S ribosomal protein L23 / 40S ribosomal protein S4 / Ribosomal protein L14p/L23e / 40S ribosomal protein S26 / 60S ribosomal protein L35a / 40S ribosomal protein S27 / 40S ribosomal protein S7 / 60S ribosomal protein L18a / 40S ribosomal protein S21 / 40S ribosomal protein S6 / 60S ribosomal protein L18 / 40S ribosomal protein S19 / Small ribosomal subunit protein uS2 / Ribosomal protein L37 / Ribosomal protein L6e / Ribosomal protein L37a / Ribosomal protein L38e / Ribosomal protein S16 / Ribosomal protein L9 / 60S ribosomal protein L13 / Small ribosomal subunit protein uS5 / Ribosomal protein L14 / 40S ribosomal protein S25 / Ribosomal protein L31 / Ribosomal protein L35 / 40S ribosomal protein S5 / 40S ribosomal protein S8 / Ribosomal protein L10 / 60S ribosomal protein L7a / Ribosomal protein S8 family protein / Ribosomal protein L21 / Ribosomal protein L2 family protein / Ribosomal protein L13 / 60S ribosomal protein L36 / 40S ribosomal subunit protein S9 / 40S ribosomal protein S3 / Large ribosomal subunit protein eL22 / Receptor for activated C kinase, RACK protein / 60S ribosomal protein L39 / 40S ribosomal protein S24 protein / Small ribosomal subunit protein uS10 / 40S ribosomal subunit protein S14 / Large ribosomal subunit protein uL22 / Ribosomal protein L19 / Small ribosomal subunit protein eS1 / 60S ribosomal protein L32 / Ribosomal protein L24e / Ribosomal protein L15 / Ribosomal protein L7Ae containing protein / 40S ribosomal protein S30 / 60S ribosomal protein L7 / 60S ribosomal protein L11 / 60S ribosomal protein L44 protein / 40S ribosomal protein S18 / Ubiquitin / ribosomal protein CEP52 / Ribosomal protein L34 / Ribosomal L27e protein family protein / Ribosomal L18p/L5e family protein / 60S ribosomal protein L29 / 40S ribosomal protein S28 / Ribosomal protein L15 / Small ribosomal subunit protein uS17 / 40S ribosomal protein S15 / Ribosomal protein RPL4A / Ribosomal protein L3 / 40S ribosomal protein S13
Similarity search - Component
Biological speciesBabesia divergens (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGutierrez-Vargas, C. / Izhaki-Tavor, L.S. / Leger-Abraham, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21AI178196-02 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007061 United States
CitationJournal: bioRxiv / Year: 2025
Title: Ribosomal Architecture and rRNA Modification Landscape in the Tick-Borne Parasite .
Authors: Cristina Gutierrez-Vargas / Lee S Izhaki-Tavor / Diana Calvopina-Chavez / Caroline D Keroack / Pablo Copello / Manoj T Duraisingh / Mélissa Léger-Abraham /
Abstract: is a tick-borne intracellular apicomplexan parasite responsible for diseases ranging from mild to fatal, with a broadening geographic distribution. Due to the complex life cycle of species, their ... is a tick-borne intracellular apicomplexan parasite responsible for diseases ranging from mild to fatal, with a broadening geographic distribution. Due to the complex life cycle of species, their survival depends on the precise control of gene expression, which is primarily regulated by epigenetic, transcriptional, and post-transcriptional mechanisms. High-resolution structural information on key components of the translation machinery, such as ribosomes, could aid in the development of antiparasitic drugs. Here, we report cryo-EM ribosome structures (2.6 Å) from the tick-borne apicomplexan pathogen , showing associated tRNAs, an mRNA fragment, and RACK1, a signaling scaffold crucial to translation regulation. Density map analysis displays ribosome regions at atomic resolution (1.7 Å), which, when combined with nanopore sequencing, enabled the comprehensive identification of rRNA modifications, including modifications unreported in other organisms. The new rRNA modifications localize not only to the reduced rRNA expansion segments but also to functionally essential ribosomal sites, uncovering new avenues for therapeutic intervention against babesiosis.
History
DepositionOct 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
SP: 40S ribosomal protein uS12
SX: 40S ribosomal protein eS19
SU: 40S ribosomal protein uS17
SL: 40S ribosomal protein uS9
SR: 40S ribosomal protein uS13
SH: 40S ribosomal protein uS7
ST: 40S ribosomal protein uS15
SA: 40S ribosomal protein eS1
SN: 40S ribosomal protein eS10
SJ: 40S ribosomal protein uS8
SI: 40S ribosomal protein eS7
SK: 40S ribosomal protein eS8
SG: 40S ribosomal protein eS6
SM: 40S ribosomal protein uS10
Se: 40S ribosomal protein eS30
SS: 40S ribosomal protein uS14
Sd: 40S ribosomal protein eS28
SC: 40S ribosomal protein uS3
SW: 40S ribosomal protein uS19
SB: 40S ribosomal protein uS2
SF: 40S ribosomal protein uS5
Sb: 40S ribosomal protein eS26
SV: 40S ribosomal protein eS17
SO: 40S ribosomal protein uS11
SZ: 40S ribosomal protein eS24
Sa: 40S ribosomal protein eS25
SQ: 40S ribosomal protein eS12
SD: 40S ribosomal protein uS4
Sf: 40S ribosomal protein eS31
Sc: 40S ribosomal protein eS27
S1: 18S ribosomal RNA
LM: 60S ribosomal protein uL15
LS: 60S ribosomal protein eL20
Le: 60S ribosomal protein eL31
Lf: 60S ribosomal protein eL32
Lj: 60S ribosomal protein eL37
LQ: 60S ribosomal protein eL18
LB: 60S ribosomal protein uL2
LI: 60S ribosomal protein uL13
LJ: 60S ribosomal protein eL13
LX: 60S ribosomal protein uL24
La: 60S ribosomal protein uL29
LD: 60S ribosomal protein uL4
LP: 60S ribosomal protein uL18
LZ: 60S ribosomal protein eL27
LU: 60S ribosomal protein uL22
LH: 60S ribosomal protein eL8
LC: 60S ribosomal protein uL3
LL: 60S ribosomal protein eL14
LK: 60S ribosomal protein uL14
LW: 60S ribosomal protein uL23
Li: 60S ribosomal protein eL36
Lm: 60S ribosomal protein eL40
LT: 60S ribosomal protein eL21
Lo: 60S ribosomal protein eL42
Ll: 60S ribosomal protein eL39
LR: 60S ribosomal protein eL19
LE: 60S ribosomal protein uL5
LO: 60S ribosomal protein uL16
LN: 60S ribosomal protein eL15
Lg: 60S ribosomal protein eL33
Lc: 60S ribosomal protein uL30
LV: 60S ribosomal protein eL22
Ld: 60S ribosomal protein eL30
Lp: 60S ribosomal protein eL43
Lb: 60S ribosomal protein eL29
Lh: 60S ribosomal protein eL34
LY: 60S ribosomal protein eL24
LG: 60S ribosomal protein eL6
Ln: 60S ribosomal protein eL41
L3: 5S ribosomal RNA
L4: 5.8S ribosomal RNA
L5: 28S ribosomal RNA
S7: E-site tRNA
S8: P-site tRNA
S9: A-site tRNA
S6: mRNA fragment
SY: 40S ribosomal protein eS21
SE: 40S ribosomal protein eS4
Sg: Receptor for activated C kinase 1, RACK1 protein
LF: 60S ribosomal protein uL6
Lk: 60S ribosomal protein eL38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,162,974218
Polymers3,159,49182
Non-polymers3,483136
Water00
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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40S ribosomal protein ... , 32 types, 32 molecules SPSXSUSLSRSHSTSASNSJSISKSGSMSeSSSdSCSWSBSFSbSVSOSZSaSQSDSfScSYSE

#1: Protein 40S ribosomal protein uS12


Mass: 16201.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987
#2: Protein 40S ribosomal protein eS19 / eS19


Mass: 20157.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G7X0
#3: Protein 40S ribosomal protein uS17 / 40S ribosomal protein S11


Mass: 18190.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LJ91
#4: Protein 40S ribosomal protein uS9 / uS9


Mass: 16708.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GAG7
#5: Protein 40S ribosomal protein uS13 / uS13


Mass: 17521.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LGT5
#6: Protein 40S ribosomal protein uS7 / uS7


Mass: 21552.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GEF4
#7: Protein 40S ribosomal protein uS15 / uS15


Mass: 17455.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LME6
#8: Protein 40S ribosomal protein eS1 / eS1


Mass: 30101.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LDG8
#9: Protein 40S ribosomal protein eS10 / eS10


Mass: 13146.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G6F1
#10: Protein 40S ribosomal protein uS8 / uS8


Mass: 14857.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GFS8
#11: Protein 40S ribosomal protein eS7 / eS7


Mass: 22069.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G7G2
#12: Protein 40S ribosomal protein eS8 / eS8


Mass: 21948.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GEV3
#13: Protein 40S ribosomal protein eS6 / eS6


Mass: 27559.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G7P5
#14: Protein 40S ribosomal protein uS10 / 40S ribosomal protein S20


Mass: 13527.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GIF9
#15: Protein 40S ribosomal protein eS30 / eS30


Mass: 6826.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LEP0
#16: Protein 40S ribosomal protein uS14 / uS14


Mass: 7511.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G696
#17: Protein 40S ribosomal protein eS28 / eS28


Mass: 7500.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LI57
#18: Protein 40S ribosomal protein uS3 / uS3


Mass: 24788.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GHF5
#19: Protein 40S ribosomal protein uS19 / uS19


Mass: 17246.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LKW7
#20: Protein 40S ribosomal protein uS2 / uS2


Mass: 31067.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G821
#21: Protein 40S ribosomal protein uS5 / 40S ribosomal protein S2


Mass: 21103.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GAQ1
#22: Protein 40S ribosomal protein eS26 / eS26


Mass: 13262.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G6Q6
#23: Protein 40S ribosomal protein eS17


Mass: 15455.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: eS17 was not identified in B. divergens 1802A. However, P. falciparum PF3D7_1242700 identified B. bovis sequence BBOV_III001250. This latter sequence was used as a blast search against the B. ...Details: eS17 was not identified in B. divergens 1802A. However, P. falciparum PF3D7_1242700 identified B. bovis sequence BBOV_III001250. This latter sequence was used as a blast search against the B. divergens Rouen strain, which identified the supercontig CCSG02000001.1: 1890202..1890772. This is the sequence, which was built in the density, and for which the sequence is provided.
Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987
#24: Protein 40S ribosomal protein uS11


Mass: 16683.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GIK0
#25: Protein 40S ribosomal protein eS24 / eS24


Mass: 15640.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GHQ4
#26: Protein 40S ribosomal protein eS25 / eS25


Mass: 11915.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GCU0
#27: Protein 40S ribosomal protein eS12 / eS12


Mass: 14716.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G6I1
#28: Protein 40S ribosomal protein uS4 / uS4


Mass: 21626.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GHC8
#29: Protein 40S ribosomal protein eS31


Mass: 8897.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G6D6
#30: Protein 40S ribosomal protein eS27 / eS27


Mass: 9160.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G7D5
#78: Protein 40S ribosomal protein eS21 / eS21


Mass: 8720.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G7M4
#79: Protein 40S ribosomal protein eS4 / eS4


Mass: 30192.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G6P4

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RNA chain , 8 types, 8 molecules S1L3L4L5S7S8S9S6

#31: RNA chain 18S ribosomal RNA


Mass: 556050.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: GenBank: 55709804
#71: RNA chain 5S ribosomal RNA


Mass: 39408.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987
#72: RNA chain 5.8S ribosomal RNA


Mass: 50949.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: GenBank: 149798938
#73: RNA chain 28S ribosomal RNA


Mass: 1072725.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987
#74: RNA chain E-site tRNA


Mass: 23774.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: E-site tRNA from PDB 9BUP / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987
#75: RNA chain P-site tRNA


Mass: 24496.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P-site tRNA from PDB 9BUP / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987
#76: RNA chain A-site tRNA


Mass: 24399.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: A-site tRNA from PDB 9BUP with anticodon adjusted to CUU(nucleotides 34-36)
Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987
#77: RNA chain mRNA fragment


Mass: 3407.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987

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60S ribosomal protein ... , 41 types, 41 molecules LMLSLeLfLjLQLBLILJLXLaLDLPLZLULHLCLLLKLWLiLmLTLoLlLRLELOLNLg...

#32: Protein 60S ribosomal protein uL15 / uL15


Mass: 16598.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LED4
#33: Protein 60S ribosomal protein eL20 / eL20


Mass: 21649.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G7I0
#34: Protein 60S ribosomal protein eL31 / eL31


Mass: 13711.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GDM1
#35: Protein 60S ribosomal protein eL32 / eL32


Mass: 15497.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LDR2
#36: Protein 60S ribosomal protein eL37 / eL37


Mass: 10982.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G827
#37: Protein 60S ribosomal protein eL18 / eL18


Mass: 24357.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G7R0
#38: Protein 60S ribosomal protein uL2 / uL2


Mass: 27998.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GFV9
#39: Protein 60S ribosomal protein uL13 / uL13


Mass: 23326.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GH72
#40: Protein 60S ribosomal protein eL13 / eL13


Mass: 22948.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GAJ7
#41: Protein 60S ribosomal protein uL24 / uL24


Mass: 16119.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G6E2
#42: Protein 60S ribosomal protein uL29 / uL29


Mass: 14473.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GDQ8
#43: Protein 60S ribosomal protein uL4 / uL4


Mass: 39509.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LL09
#44: Protein 60S ribosomal protein uL18 / uL18


Mass: 35365.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LI25
#45: Protein 60S ribosomal protein eL27 / eL27


Mass: 16799.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LI24
#46: Protein 60S ribosomal protein uL22 / 60S ribosomal protein L17


Mass: 22143.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GIZ6
#47: Protein 60S ribosomal protein eL8 / eL8


Mass: 32207.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GFQ9
#48: Protein 60S ribosomal protein uL3 / uL3


Mass: 44597.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LLF8
#49: Protein 60S ribosomal protein eL14 / eL14


Mass: 14909.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GCK1
#50: Protein 60S ribosomal protein uL14 / uL14


Mass: 14816.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G6Q1
#51: Protein 60S ribosomal protein uL23 / uL23


Mass: 17344.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G6J7
#52: Protein 60S ribosomal protein eL36 / eL36


Mass: 13093.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GH83
#53: Protein 60S ribosomal protein eL40


Mass: 6393.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LH16
#54: Protein 60S ribosomal protein eL21 / eL21


Mass: 18438.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GFV7
#55: Protein 60S ribosomal protein eL42 / eL42


Mass: 12011.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LG33
#56: Protein 60S ribosomal protein eL39 / eL39


Mass: 7173.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GHL1
#57: Protein 60S ribosomal protein eL19 / eL19


Mass: 22632.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GKV3
#58: Protein 60S ribosomal protein uL5 / uL5


Mass: 19797.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LFK3
#59: Protein 60S ribosomal protein uL16 / uL16


Mass: 25790.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GFA1
#60: Protein 60S ribosomal protein eL15


Mass: 24502.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LIN3
#61: Protein 60S ribosomal protein eL33 / eL33


Mass: 13346.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G6T1
#62: Protein 60S ribosomal protein uL30 / uL30


Mass: 30421.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LFB9
#63: Protein 60S ribosomal protein eL22 / 60S ribosomal protein L22


Mass: 14211.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GHH1
#64: Protein 60S ribosomal protein eL30 / eL30


Mass: 11965.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LEI7
#65: Protein 60S ribosomal protein eL43 / eL43


Mass: 10612.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G9R3
#66: Protein 60S ribosomal protein eL29 / eL29


Mass: 6820.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LI35
#67: Protein 60S ribosomal protein eL34 / eL34


Mass: 17022.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LHM2
#68: Protein 60S ribosomal protein eL24 / eL24


Mass: 17452.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LE14
#69: Protein 60S ribosomal protein eL6 / eL6


Mass: 23708.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9G923
#70: Protein/peptide 60S ribosomal protein eL41


Mass: 5136.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Using T. gondii as a reference sequence (TGME49_213580), led us to identify the unannotated genomic sequence corresponding to eL41 in the B. divergens 1802 reference strain (JAHBMH010000034: ...Details: Using T. gondii as a reference sequence (TGME49_213580), led us to identify the unannotated genomic sequence corresponding to eL41 in the B. divergens 1802 reference strain (JAHBMH010000034: 30674..30988 supercontig).
Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987
#81: Protein 60S ribosomal protein uL6 / uL6


Mass: 21426.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GAI9
#82: Protein 60S ribosomal protein eL38 / eL38


Mass: 8077.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GAA9

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Protein , 1 types, 1 molecules Sg

#80: Protein Receptor for activated C kinase 1, RACK1 protein


Mass: 35573.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GHI1

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Non-polymers , 2 types, 136 molecules

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


Mass: 24.305 Da / Num. of mol.: 124 / Source method: obtained synthetically / Formula: Mg
#84: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K

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Details

Has ligand of interestN
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

Component
IDNameTypeEntity IDParent-IDSource
180S ribosomeRIBOSOME#1-#820NATURAL
240SCOMPLEX#39-#43, #81, #44-#68, #82, #70, #731NATURAL
360SCOMPLEX#1-#3, #78-#79, #4-#13, #80, #14-#38, #69, #71-#721NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Babesia divergens (eukaryote)32595Rouen 1987
32Babesia divergens (eukaryote)32595Rouen 1987
43Babesia divergens (eukaryote)32595Rouen 1987
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMPotassium acetateKCH3COO1
310 mMAmmonium acetateNH4CH3COO1
410 mMMagnesium acetateMg(CH3COO)21
55 mM2-MercaptoethanolHSCH2CH2OH1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid had an additional ultrathin continous carbon layer (2 nm)
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.4 sec. / Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 12144

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2PHENIX1.21.2_5419+SVNmodel refinement
3EPUimage acquisition
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1259788
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26467 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Protein chains were built de novo with ModelAngelo. The rRNA chains from PDB 9YGM, which corresponds to the highest-resolution conformational class (3DC3, 80S with E-site tRNA) from the same ...Details: Protein chains were built de novo with ModelAngelo. The rRNA chains from PDB 9YGM, which corresponds to the highest-resolution conformational class (3DC3, 80S with E-site tRNA) from the same dataset, were rigid-body fit and remodeled. The complete model then underwent iterative rounds of manual adjustment in Coot and real-space refinement in Phenix.
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDDetails (eV)Source nameTypeAccession codeChain-IDInitial refinement model-ID
1ribosomal proteinsOtherin silico model
29YGM

9ygm

L35SPDBexperimental model9YGML32
39YGM

9ygm

L45.8SPDBexperimental model9YGML42
49YGM

9ygm

L528S rRNAPDBexperimental model9YGML52
59YGM

9ygm

S118S rRNAPDBexperimental model9YGMS12

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