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

ID or keywords:

Entry

Database: PDB / ID: 9ygm

Title

Babesia divergens ribosome structure by single-particle cryo-EM (3D class3, E-site tRNA)

Components

(40S ribosomal protein ...) x 32
(60S ribosomal protein ...) x 42
18S ribosomal RNA
28S ribosomal RNA
5.8S ribosomal RNA
5S ribosomal RNA
E-site tRNA
Receptor for activated C kinase 1, RACK1 protein

Keywords

RIBOSOME / 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 ...
Similarity search - Function

: / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / Ribosomal protein S26e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site ...: / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / 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 L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / 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
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 / Plectin/S10 domain containing 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 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 L1 / 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 species

Babesia divergens (eukaryote)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å

Authors

Gutierrez-Vargas, C. / Izhaki-Tavor, L.S. / Leger-Abraham, M.

Funding support

United States, 2items

Organization	Grant number	Country
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

Citation

Journal: 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

Deposition	Sep 29, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 24, 2026	Provider: repository / Type: Initial release
Revision 1.0	Jun 24, 2026	Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0	Jun 24, 2026	Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0	Jun 24, 2026	Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0	Jun 24, 2026	Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ygm.cif.gz	5.4 MB	Display	PDBx/mmCIF format
PDB format	pdb9ygm.ent.gz		Display	PDB format
PDBx/mmJSON format	9ygm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yg/9ygm ftp://data.pdbj.org/pub/pdb/validation_reports/yg/9ygm	HTTPS FTP

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Related structure data

Related structure data	72933MC 73574C 73576C 73577C 73581C 73602C 9yxbC 72052 72055 72069 72070 M: map data used to model this data C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (79) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (8) #10 - Oct 2000 Ribosome similarity (75) #260 - Aug 2021 Ribonuclease P similarity (7) #253 - Jan 2021 Expressome similarity (3) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #161 - May 2013 Ricin similarity (203) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (90) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (3) #245 - May 2020 Spliceosomes similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (3) #65 - May 2005 Self-splicing RNA similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #227 - Nov 2018 Telomerase similarity (2) #104 - Aug 2008 Selenocysteine Synthase similarity (2) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #60 - Dec 2004 Ubiquitin similarity (4) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
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Deposited unit

L3: 5S ribosomal RNA

LB: 60S ribosomal protein uL2

LC: 60S ribosomal protein uL3

LE: 60S ribosomal protein uL5

LF: 60S ribosomal protein uL6

LG: 60S ribosomal protein eL6

LJ: 60S ribosomal protein eL13

LK: 60S ribosomal protein uL14

LP: 60S ribosomal protein uL18

LQ: 60S ribosomal protein eL18

LU: 60S ribosomal protein uL22

LV: 60S ribosomal protein eL22

LZ: 60S ribosomal protein eL27

La: 60S ribosomal protein uL29

Lb: 60S ribosomal protein eL29

Ld: 60S ribosomal protein eL30

Le: 60S ribosomal protein eL31

Lf: 60S ribosomal protein eL32

Lg: 60S ribosomal protein eL33

LD: 60S ribosomal protein uL4

LI: 60S ribosomal protein uL13

LL: 60S ribosomal protein eL14

LM: 60S ribosomal protein uL15

LN: 60S ribosomal protein eL15

LO: 60S ribosomal protein uL16

LR: 60S ribosomal protein eL19

LS: 60S ribosomal protein eL20

LT: 60S ribosomal protein eL21

LX: 60S ribosomal protein uL24

Lc: 60S ribosomal protein uL30

Lh: 60S ribosomal protein eL34

Li: 60S ribosomal protein eL36

Lj: 60S ribosomal protein eL37

Lk: 60S ribosomal protein eL38

Ll: 60S ribosomal protein eL39

Lm: 60S ribosomal protein eL40

Lp: 60S ribosomal protein eL43

Lo: 60S ribosomal protein eL42

LH: 60S ribosomal protein eL8

SA: 40S ribosomal protein eS1

SB: 40S ribosomal protein uS2

SD: 40S ribosomal protein uS4

SE: 40S ribosomal protein eS4

SF: 40S ribosomal protein uS5

SG: 40S ribosomal protein eS6

SI: 40S ribosomal protein eS7

SJ: 40S ribosomal protein uS8

SK: 40S ribosomal protein eS8

SP: 40S ribosomal protein uS12

ST: 40S ribosomal protein uS15

SU: 40S ribosomal protein uS17

SY: 40S ribosomal protein eS21

Sb: 40S ribosomal protein eS26

Sc: 40S ribosomal protein eS27

Se: 40S ribosomal protein eS30

SC: 40S ribosomal protein uS3

SH: 40S ribosomal protein uS7

SL: 40S ribosomal protein uS9

SM: 40S ribosomal protein uS10

SQ: 40S ribosomal protein eS12

SR: 40S ribosomal protein uS13

SS: 40S ribosomal protein uS14

SW: 40S ribosomal protein uS19

Sd: 40S ribosomal protein eS28

Sg: Receptor for activated C kinase 1, RACK1 protein

SN: 40S ribosomal protein eS10

SZ: 40S ribosomal protein eS24

Sa: 40S ribosomal protein eS25

Sf: 40S ribosomal protein eS31

Ln: 60S ribosomal protein eL41

SV: 40S ribosomal protein eS17

SO: 40S ribosomal protein uS11

L4: 5.8S ribosomal RNA

L5: 28S ribosomal RNA

S7: E-site tRNA

S1: 18S ribosomal RNA

LA: 60S ribosomal protein uL1

LW: 60S ribosomal protein uL23

LY: 60S ribosomal protein eL24

SX: 40S ribosomal protein eS19

hetero molecules

3.14 MDa, 80 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

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RNA chain , 5 types, 5 molecules L3L4L5S7S1

#1: 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
#73: RNA chain	5.8S ribosomal RNA Mass: 50963.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: GenBank: 149798938
#74: RNA chain	28S ribosomal RNA Mass: 1073104.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987
#75: RNA chain	E-site tRNA Mass: 23774.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The E-site tRNA (PDB 3J7A) was docked into the ribosome using ChimeraX and further refined in PHENIX. Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987
#76: RNA chain	18S ribosomal RNA Mass: 556419.688 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 ... , 42 types, 42 molecules LBLCLELFLGLJLKLPLQLULVLZLaLbLdLeLfLgLDLILLLMLNLOLRLSLTLXLcLh...

#2: 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
#3: 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
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: Protein	60S ribosomal protein 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
#30: Protein	60S ribosomal protein 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
#31: Protein	60S ribosomal protein 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
#32: Protein	60S ribosomal protein 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
#33: Protein	60S ribosomal protein 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
#34: Protein	60S ribosomal protein 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
#35: Protein	60S ribosomal protein 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
#36: 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
#37: Protein	60S ribosomal protein 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
#38: Protein	60S ribosomal protein 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
#39: Protein	60S ribosomal protein 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
#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
#77: Protein	60S ribosomal protein uL1 Mass: 24471.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9LDZ3
#78: 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
#79: 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

+
40S ribosomal protein ... , 32 types, 32 molecules SASBSDSESFSGSISJSKSPSTSUSYSbScSeSCSHSLSMSQSRSSSWSdSNSZSaSfSVSOSX

#40: Protein	40S ribosomal protein 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
#41: Protein	40S ribosomal protein 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
#42: Protein	40S ribosomal protein 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
#43: Protein	40S ribosomal protein 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
#44: 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
#45: Protein	40S ribosomal protein 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
#46: Protein	40S ribosomal protein 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
#47: Protein	40S ribosomal protein 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
#48: Protein	40S ribosomal protein 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
#49: 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
#50: Protein	40S ribosomal protein 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
#51: 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
#52: Protein	40S ribosomal protein 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
#53: Protein	40S ribosomal protein 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
#54: Protein	40S ribosomal protein 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
#55: Protein	40S ribosomal protein 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
#56: Protein	40S ribosomal protein 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
#57: Protein	40S ribosomal protein uS7 Mass: 21552.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987
#58: Protein	40S ribosomal protein 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
#59: 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
#60: Protein	40S ribosomal protein 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
#61: Protein	40S ribosomal protein 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
#62: Protein	40S ribosomal protein 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
#63: Protein	40S ribosomal protein 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
#64: 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
#66: 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
#67: 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
#68: 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
#69: 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
#71: 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
#72: 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
#80: 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

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Protein , 1 types, 1 molecules Sg

#65: Protein	Receptor for activated C kinase 1, RACK1 protein Mass: 35573.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Receptor for Activated C Kinase 1 / Source: (natural) Babesia divergens (eukaryote) / Strain: Rouen 1987 / References: UniProt: A0AAD9GHI1

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Non-polymers , 4 types, 201 molecules

#81: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 136 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#82: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#83: Chemical	... ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#84: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component

Name: 80S ribosome / Type: RIBOSOME / Entity ID: #1-#63, #80, #64-#79 / Source: NATURAL

Source (natural)

Organism:

Babesia divergens (eukaryote) / Strain: Rouen 1987

Buffer solution

pH: 7.4

Buffer component

ID	Conc.	Name	Buffer-ID
1	20 mM	HEPES	1
2	150 mM	Potassium acetate	1
3	10 mM	Ammonium acetate	1
4	10 mM	Magnesium acetate	1
5	5 mM	2-mercaptoethanol	1

Specimen

Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES

Specimen support

Details: The grid had an additional ultrathin continuous carbon layer (2 nm)
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3

Vitrification

Instrument: 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
Microscopy	Model: TFS KRIOS
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: 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 holder	Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording	Average 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

ID	Name	Version	Category
1	crYOLO		particle selection
2	SerialEM		image acquisition
9	PHENIX	1.21.2_5419+SVN	model refinement
13	RELION	30001	3D reconstruction

CTF correction

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

Particle selection

Num. of particles selected: 1259788

3D reconstruction

Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 261009 / Num. of class averages: 1 / Symmetry type: POINT

Atomic model building

Protocol: RIGID BODY FIT
Details: Initial docking and fitting was done in UCSF ChimeraX for the ribosomal proteins using AlphaFold2 predicted models, except for eL41; the T. gondii eL41 chain (PDB 5XXB) served as the initial ...

Atomic model building

3D fitting-ID: 1

ID	PDB-ID	Pdb chain-ID	Details (eV)	Source name	Type	Accession code	Chain-ID	Initial refinement model-ID
1			ribosomal proteins	AlphaFold	in silico model
2	5XXU 5xxu	A	initial model consisted of conserved 18S regions	PDB	experimental model	5XXU	A	2
3	5XXB 5xxb	A	initial model consisted of conserved 28S regions	PDB	experimental model	5XXB	A	3
4	5XXB 5xxb	B	initial model consisted of conserved 5S regions	PDB	experimental model	5XXB	B	3
5	5XXB 5xxb	C	initial model consisted of conserved 5.8S regions	PDB	experimental model	5XXB	C	3
6	5XXB 5xxb	m	eL41	PDB	experimental model	5XXB	m	3
7	3J7A 3j7a	7	E-site tRNA	PDB	experimental model	3J7A	7	4

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RNA chain , 5 types, 5 molecules L3L4L5S7S1

+
60S ribosomal protein ... , 42 types, 42 molecules LBLCLELFLGLJLKLPLQLULVLZLaLbLdLeLfLgLDLILLLMLNLOLRLSLTLXLcLh...

+
40S ribosomal protein ... , 32 types, 32 molecules SASBSDSESFSGSISJSKSPSTSUSYSbScSeSCSHSLSMSQSRSSSWSdSNSZSaSfSVSOSX

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Protein , 1 types, 1 molecules Sg

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Non-polymers , 4 types, 201 molecules

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-RNA chain , 5 types, 5 molecules L3L4L5S7S1

+60S ribosomal protein ... , 42 types, 42 molecules LBLCLELFLGLJLKLPLQLULVLZLaLbLdLeLfLgLDLILLLMLNLOLRLSLTLXLcLh...

+40S ribosomal protein ... , 32 types, 32 molecules SASBSDSESFSGSISJSKSPSTSUSYSbScSeSCSHSLSMSQSRSSSWSdSNSZSaSfSVSOSX

-Protein , 1 types, 1 molecules Sg

-Non-polymers , 4 types, 201 molecules

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RNA chain , 5 types, 5 molecules L3L4L5S7S1

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60S ribosomal protein ... , 42 types, 42 molecules LBLCLELFLGLJLKLPLQLULVLZLaLbLdLeLfLgLDLILLLMLNLOLRLSLTLXLcLh...

+
40S ribosomal protein ... , 32 types, 32 molecules SASBSDSESFSGSISJSKSPSTSUSYSbScSeSCSHSLSMSQSRSSSWSdSNSZSaSfSVSOSX

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Protein , 1 types, 1 molecules Sg

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Non-polymers , 4 types, 201 molecules

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Experimental details

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Experiment

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