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- PDB-9fia: SSU(body) structure derived from the SSU sample of the mitoriboso... -

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Basic information

Entry
Database: PDB / ID: 9fia
TitleSSU(body) structure derived from the SSU sample of the mitoribosome from T. gondii.
Components
  • (30S ribosomal protein ...) x 2
  • (Mitochondrial ribosomal protein, ...) x 11
  • (Putative 30S ribosomal protein ...) x 2
  • (Putative ribosomal protein ...) x 2
  • (Ribosomal protein ...) x 2
  • (Ribosomal protein, ...) x 3
  • (unidentified ...) x 12
  • Acylphosphatase-like domain-containing protein
  • CHCH domain-containing protein
  • DnaJ domain-containing protein
  • Enoyl-CoA hydratase/isomerase family protein
  • Macro domain-containing protein
  • Pentatricopeptide repeat domain-containing protein
  • Putative homeodomain containing protein
  • Putative mitochondrial ribosomal protein s6-2
  • RAP domain-containing protein
  • RNA13
  • RNA15
  • RNA17
  • RNA19
  • RNA30
  • RNA33
  • RNA5
  • RNA8
  • SSUA
  • SSUB
  • SSUE
  • SSUF
  • ulr11
  • ulr12
  • ulr13
  • ulr14
  • ulr15
  • ulr16
  • ulr17
  • ulr19
  • ulr20
  • ulr21
  • url18
KeywordsRIBOSOME / Complex / translation / rRNA
Function / homology
Function and homology information


hydro-lyase activity / mitochondrial small ribosomal subunit / mitochondrial translation / fatty acid metabolic process / isomerase activity / small ribosomal subunit / small ribosomal subunit rRNA binding / ribosome / structural constituent of ribosome / translation ...hydro-lyase activity / mitochondrial small ribosomal subunit / mitochondrial translation / fatty acid metabolic process / isomerase activity / small ribosomal subunit / small ribosomal subunit rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mitochondrion / DNA binding / RNA binding / cytoplasm
Similarity search - Function
: / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / ClpP/crotonase-like domain superfamily / Homeobox-like domain superfamily / Ribosomal protein S6, plastid/chloroplast ...: / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / ClpP/crotonase-like domain superfamily / Homeobox-like domain superfamily / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Putative ribosomal protein S17 / Acylphosphatase-like domain-containing protein / Uncharacterized protein / Uncharacterized protein ...RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Putative ribosomal protein S17 / Acylphosphatase-like domain-containing protein / Uncharacterized protein / Uncharacterized protein / Putative homeodomain containing protein / Uncharacterized protein / CHCH domain-containing protein / Putative 30S ribosomal protein S15 / Putative ribosomal protein S8 / Uncharacterized protein / Putative mitochondrial ribosomal protein s6-2 / DnaJ domain-containing protein / Putative 30S ribosomal protein S16 / Enoyl-CoA hydratase/isomerase family protein / 30S ribosomal protein S12, putative / Uncharacterized protein / Pentatricopeptide repeat domain-containing protein / 30S ribosomal protein S5, putative / Ribosomal protein S11, putative / Ribosomal protein S18, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Macro domain-containing protein / RAP domain-containing protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsRocha, R.E.O. / Barua, S. / Boissier, F. / Nguyen, T.T. / Hashem, Y.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission101088541European Union
CitationJournal: Nat Commun / Year: 2024
Title: Apicomplexan mitoribosome from highly fragmented rRNAs to a functional machine.
Authors: Chaoyue Wang / Sari Kassem / Rafael Eduardo Oliveira Rocha / Pei Sun / Tan-Trung Nguyen / Joachim Kloehn / Xianyong Liu / Lorenzo Brusini / Alessandro Bonavoglia / Sramona Barua / Fanny ...Authors: Chaoyue Wang / Sari Kassem / Rafael Eduardo Oliveira Rocha / Pei Sun / Tan-Trung Nguyen / Joachim Kloehn / Xianyong Liu / Lorenzo Brusini / Alessandro Bonavoglia / Sramona Barua / Fanny Boissier / Mayara Lucia Del Cistia / Hongjuan Peng / Xinming Tang / Fujie Xie / Zixuan Wang / Oscar Vadas / Xun Suo / Yaser Hashem / Dominique Soldati-Favre / Yonggen Jia /
Abstract: The phylum Apicomplexa comprises eukaryotic parasites that cause fatal diseases affecting millions of people and animals worldwide. Their mitochondrial genomes have been significantly reduced, ...The phylum Apicomplexa comprises eukaryotic parasites that cause fatal diseases affecting millions of people and animals worldwide. Their mitochondrial genomes have been significantly reduced, leaving only three protein-coding genes and highly fragmented mitoribosomal rRNAs, raising challenging questions about mitoribosome composition, assembly and structure. Our study reveals how Toxoplasma gondii assembles over 40 mt-rRNA fragments using exclusively nuclear-encoded mitoribosomal proteins and three lineage-specific families of RNA-binding proteins. Among these are four proteins from the Apetala2/Ethylene Response Factor (AP2/ERF) family, originally known as transcription factors in plants and Apicomplexa, now repurposed as essential mitoribosome components. Cryo-EM analysis of the mitoribosome structure demonstrates how these AP2 proteins function as RNA binders to maintain mitoribosome integrity. The mitoribosome is also decorated with members of lineage-specific RNA-binding proteins belonging to RAP (RNA-binding domain abundant in Apicomplexa) proteins and HPR (heptatricopeptide repeat) families, highlighting the unique adaptations of these parasites. Solving the molecular puzzle of apicomplexan mitoribosome could inform the development of therapeutic strategies targeting organellar translation.
History
DepositionMay 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B0: Mitochondrial ribosomal protein, mS145
B1: unidentified peptide
B2: Ribosomal protein S18, putative
B3: Mitochondrial ribosomal protein, mS23
B4: CHCH domain-containing protein
B5: Ribosomal protein S11, putative
B6: Putative mitochondrial ribosomal protein s6-2
B7: unidentified peptide
B8: unidentified peptide
B9: DnaJ domain-containing protein
BA: Mitochondrial ribosomal protein, mS137
BB: RAP domain-containing protein
BC: Mitochondrial ribosomal protein, mS47
BD: Pentatricopeptide repeat domain-containing protein
BE: Mitochondrial ribosomal protein, mS140
BF: Mitochondrial ribosomal protein, mS147
BG: Ribosomal protein, uS2m
BH: Putative ribosomal protein S8
BI: unidentified peptide
BJ: unidentified peptide
BK: Mitochondrial ribosomal protein, mS26
BL: Putative ribosomal protein S17
BN: unidentified peptide
BO: Putative 30S ribosomal protein S15
BP: unidentified peptide
BQ: Macro domain-containing protein
BS: Ribosomal protein, bS21m
BT: Mitochondrial ribosomal protein, mS156
BU: unidentified peptide
BV: Putative homeodomain containing protein
BW: Mitochondrial ribosomal protein, mS144
BX: unidentified peptide
BY: unidentified peptide
Ba: unidentified peptide
Bb: unidentified peptide
Bc: Enoyl-CoA hydratase/isomerase family protein
Bd: unidentified peptide
Be: unidentified peptide
Bg: Ribosomal protein, uS2m
Bh: Putative 30S ribosomal protein S16
Bi: Mitochondrial ribosomal protein, mS153
Bj: unidentified peptide
Bk: Mitochondrial ribosomal protein, mS26
Bl: 30S ribosomal protein S12, putative
HJ: 30S ribosomal protein S5, putative
HS: Acylphosphatase-like domain-containing protein
b1: ulr11
b2: SSUE
b3: ulr12
b4: RNA13
bA: RNA19
bD: RNA15
bE: RNA8
bG: ulr13
bH: ulr14
bI: ulr15
bJ: RNA33
bK: RNA5
bL: RNA17
bN: SSUB
bO: SSUA
bP: ulr16
bQ: ulr17
bR: RNA30
bS: url18
bT: SSUF
bU: ulr19
bV: ulr20
bY: ulr21


Theoretical massNumber of molelcules
Total (without water)2,007,93969
Polymers2,007,93969
Non-polymers00
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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Mitochondrial ribosomal protein, ... , 11 types, 11 molecules B0B3BABCBEBFBKBTBWBiBk

#1: Protein Mitochondrial ribosomal protein, mS145


Mass: 75001.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GGX8
#4: Protein Mitochondrial ribosomal protein, mS23


Mass: 41612.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A086M9R9
#11: Protein Mitochondrial ribosomal protein, mS137


Mass: 102582.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F8D3
#13: Protein Mitochondrial ribosomal protein, mS47


Mass: 44677.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GBT4
#15: Protein Mitochondrial ribosomal protein, mS140


Mass: 116977.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#16: Protein Mitochondrial ribosomal protein, mS147


Mass: 34463.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YYT2
#21: Protein Mitochondrial ribosomal protein, mS26


Mass: 59459.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A086JV31
#27: Protein Mitochondrial ribosomal protein, mS156


Mass: 30802.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#30: Protein Mitochondrial ribosomal protein, mS144


Mass: 59978.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F063
#39: Protein Mitochondrial ribosomal protein, mS153


Mass: 28704.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A2G8XVF2
#40: Protein Mitochondrial ribosomal protein, mS26


Mass: 51592.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A086KM95

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Unidentified ... , 12 types, 15 molecules B1B7B8BjBIBNBXBJBPBUBYBaBbBdBe

#2: Protein/peptide unidentified peptide


Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: unidentified peptide / Source: (natural) Toxoplasma gondii (eukaryote)
#8: Protein/peptide unidentified peptide


Mass: 1039.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Unidentified peptide 2 / Source: (natural) Toxoplasma gondii (eukaryote)
#9: Protein/peptide unidentified peptide


Mass: 1805.216 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#19: Protein/peptide unidentified peptide


Mass: 1124.378 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#20: Protein/peptide unidentified peptide


Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#24: Protein/peptide unidentified peptide


Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#28: Protein/peptide unidentified peptide


Mass: 1209.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#31: Protein/peptide unidentified peptide


Mass: 954.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#32: Protein/peptide unidentified peptide


Mass: 869.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#33: Protein/peptide unidentified peptide


Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#35: Protein/peptide unidentified peptide


Mass: 2826.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#36: Protein/peptide unidentified peptide


Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)

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Ribosomal protein ... , 2 types, 2 molecules B2B5

#3: Protein Ribosomal protein S18, putative


Mass: 84465.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F879
#6: Protein Ribosomal protein S11, putative


Mass: 43464.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F665

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Protein , 9 types, 9 molecules B4B6B9BBBDBQBVBcHS

#5: Protein CHCH domain-containing protein


Mass: 16112.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JX47
#7: Protein Putative mitochondrial ribosomal protein s6-2


Mass: 19272.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K9W0
#10: Protein DnaJ domain-containing protein


Mass: 25359.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KC34
#12: Protein RAP domain-containing protein


Mass: 168566.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GUD6
#14: Protein Pentatricopeptide repeat domain-containing protein


Mass: 74729.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F073
#25: Protein Macro domain-containing protein


Mass: 75927.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GKJ3
#29: Protein Putative homeodomain containing protein


Mass: 67147.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A151HJJ2
#34: Protein Enoyl-CoA hydratase/isomerase family protein


Mass: 80344.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KGS2
#43: Protein Acylphosphatase-like domain-containing protein


Mass: 27403.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Correct sequence: ...Details: Correct sequence: MAPFPRGIVKPRSAKVRAILNLSVEQRQPNPLRAPRKSLLDPPPCVAPLEKGNPKLDRQFDTLNRSITGFRKYKAPHTTAPRVVRDRDETNFHEMLGKFRFDLQGSFKENGDMLRDSLLQVGRDLFLVGWVKCRSRFATGHIQGDVHALSYMRRYLEKHVDESVSSVRFYEENFGMPLLEYERLSAVNDFRAPGKKQQHALRAAEKNKAKKLEQESLRHAQELERFYEENCIRNY
Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YXT0

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Ribosomal protein, ... , 3 types, 3 molecules BGBSBg

#17: Protein Ribosomal protein, uS2m


Mass: 18266.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K4L0
#26: Protein Ribosomal protein, bS21m


Mass: 28104.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8G0I7
#37: Protein Ribosomal protein, uS2m


Mass: 34172.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A151HEQ5

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Putative ribosomal protein ... , 2 types, 2 molecules BHBL

#18: Protein Putative ribosomal protein S8


Mass: 14858.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K132
#22: Protein Putative ribosomal protein S17


Mass: 14084.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YU94

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Putative 30S ribosomal protein ... , 2 types, 2 molecules BOBh

#23: Protein Putative 30S ribosomal protein S15


Mass: 44807.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JZR0
#38: Protein Putative 30S ribosomal protein S16


Mass: 19450.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KCY1

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30S ribosomal protein ... , 2 types, 2 molecules BlHJ

#41: Protein 30S ribosomal protein S12, putative


Mass: 66517.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8EUD1
#42: Protein 30S ribosomal protein S5, putative


Mass: 127333.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Right sequence (uniprot ID = S8F5G8): ...Details: Right sequence (uniprot ID = S8F5G8): MRCPLAPRRQRRLPRDSSSSVSLFLPHRGSLSLSSAFSPSFRRSPCPRSSPCLASSVPPSRLFSSASPNDSRLALKKPLSPSFSSPFAFSRYTRDPELRHLTSTSRVQAPLPLRRCAAPVASLASSPCLSSSRASSASLSPCSLASLGSRSSPFCGGSRRGGERPPCERRASAGCGAAANSFSSAPRPSRLSPSSPFFPSGLGCSSSPAHRARVAGPRLPLRSAFVALFPGQPTRTLCFPAASSALSFSAQPSPPTASASSFQSPRRLHNSHQARVLRRRHVYRDKHLDHVPTERARQLAEQRSAFELPRGTGEPLQGGSRFPGGVMAPHLRVKLEKEKFLRDCMREQENLAALFTETEKETLLGRRGDSRESHEEEPATREAEKQTSEGGKSDEAGKDGGKQEDKQGAAPFGRKLQELESFVGSALRTYRLLRPHALPFYKEDSLLSMQSKLNEATLKHSPLVHDLVELKKRNLSVPSDLLPPDFNALQFSLPVVSARGFLLALSAAANSVAEDLEFLCRRLSVPNLPHPTHPFRLKLLLDALFESFKLRKDPHYAHDWAQRNWPRLQAAMPEPLSELSADSVGLWLKAHLERVIENQRGRHADGRGRLLAQKFPLKSDEEDLYSLADDFIFDHEIVDEQFCDERLSQFPIDKAGELFRRVADFFGLTKGPQPAVNDAVVAQFQNLVYTLDEIGLSNWMKMDTREIEEFLPEGDPPSFAASQQDLDAARLLLKAAARGKANLLDFEALDPYKLLHGFDFKTVQEELATLPPNPFLTDADIDELFDITTAAVSMNQSEVAPSASLRNFKAKFGRTPLEALLDSEEKFLTSAGPVDWLKDEDENGEAFVSWRWKRPAQTVYDAEKGMFVREREGVDPLIKLHELRQTLLSVSRMMSMNKQGRVYYFRAIVAVGNGRGLFGIGIAFGPSPKEARSNAALAAIQNLDHIDFDVGRTLTTPVHGSEYSAHVKIVPRPLGKGLKSNLRYLPLLYLMGIDNCRVSFYGPSASARWFTRAKALKRALEQLQSRRTLANATGQKYDLLVAPGEHWMHWPDRWFRPISTEYARMLERIKKKRPPSYRRGFRAAIDEVIPEEIRPEFTPYTWKSPLQKWAEELKRKRLTSHNVYETEVFLHPPAQSSSPS
Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F5G8

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RNA chain , 23 types, 23 molecules b1b2b3b4bAbDbEbGbHbIbJbKbLbNbObPbQbRbSbTbUbVbY

#44: RNA chain ulr11


Mass: 2404.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#45: RNA chain SSUE


Mass: 15342.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#46: RNA chain ulr12


Mass: 1485.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#47: RNA chain RNA13


Mass: 11019.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#48: RNA chain RNA19


Mass: 10856.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#49: RNA chain RNA15


Mass: 8832.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#50: RNA chain RNA8


Mass: 34453.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#51: RNA chain ulr13


Mass: 1179.706 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#52: RNA chain ulr14


Mass: 567.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#53: RNA chain ulr15


Mass: 873.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#54: RNA chain RNA33


Mass: 22623.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#55: RNA chain RNA5


Mass: 26454.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#56: RNA chain RNA17


Mass: 15372.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#57: RNA chain SSUB


Mass: 39029.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#58: RNA chain SSUA


Mass: 36984.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#59: RNA chain ulr16


Mass: 4547.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#60: RNA chain ulr17


Mass: 4241.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#61: RNA chain RNA30


Mass: 9904.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#62: RNA chain url18


Mass: 9446.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#63: RNA chain SSUF


Mass: 19508.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: polyA at the end / Source: (natural) Toxoplasma gondii (eukaryote)
#64: RNA chain ulr19


Mass: 7609.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#65: RNA chain ulr20


Mass: 1792.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#66: RNA chain ulr21


Mass: 3322.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)

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Details

Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: LSU structure derived from the LSU sample of the mitoribosome from T. gondii.
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightValue: 4 MDa / Experimental value: YES
Source (natural)Organism: Toxoplasma gondii (eukaryote) / Cellular location: Cytoplasm / Organelle: Mitochondria
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blotting force 5, blotting time 2.5 seconds.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 95 K / Temperature (min): 90 K
Image recordingAverage exposure time: 6 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9524
Image scansSampling size: 6.35 µm / Width: 4096 / Height: 4096 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5.1particle selection
2SerialEM4.1image acquisition
4CTFFIND4CTF correction
7ISOLDE1.7model fitting
9PHENIX1.20.1-4487model refinement
12cryoSPARC4.5.1classificationHeterogeneous refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 280177
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22169 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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