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

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Basic information

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 LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome ...preribosome / 90S preribosome / protein-RNA complex assembly / translation regulator activity / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / kinase activity / rRNA processing / large ribosomal subunit / ribosomal small subunit assembly / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytoplasm / cytosol
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 S26e ...: / 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 S26e / Ribosomal protein L29e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal L29e protein family / Ribosomal protein S12e / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e signature. / 40S Ribosomal protein S10 / Ribosomal protein L10e / S27a-like superfamily / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / : / Ribosomal L40e family / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein S25 / : / S25 ribosomal protein / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L35 / Ribosomal protein L30e signature 2. / Ribosomal protein L7A/L8 / Ribosomal protein S27a / Ribosomal protein L30e, conserved site / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein L6e / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L13, eukaryotic/archaeal / 60S ribosomal protein L6E / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / : / Ribosomal protein L30/YlxQ / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L36e / 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: To Be Published
Title: Ribosomal architecture and rRNA modification landscape in the tick-borne parasite Babesia divergens
Authors: Gutierrez-Vargas, C. / Izhaki-Tavor, L.S. / Calvopina-Chavez, D. / Keroack, C. / Copello, P. / Duraisingh, M. / Leger-Abraham, M.
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
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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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