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- PDB-9i05: Cryo-EM structure of the large subunit of the mitochondrial ribos... -

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Entry
Database: PDB / ID: 9i05
TitleCryo-EM structure of the large subunit of the mitochondrial ribosome from Toxoplasma gondii
Components
  • (AP2 domain transcription factor ...) x 2
  • (LSU-32) x 2
  • (Large ribosomal subunit protein ...) x 10
  • (Putative 50S ribosomal protein ...) x 4
  • (Putative LSU ribosomal protein ...) x 2
  • (Putative ribosomal protein ...) x 3
  • (RAP domain-containing ...) x 7
  • (Ribosomal l25 family ...) x 2
  • (Ribosomal protein ...) x 4
  • (Transmembrane ...) x 2
  • 50S ribosomal protein L19, chloroplastic
  • BIR protein
  • Chain Ua
  • Chain Uc
  • Chain Ud
  • Chain Ue
  • Chain Uf
  • DUF6832 domain-containing protein
  • FAS1 domain-containing protein
  • HECT-domain (Ubiquitin-transferase) domain-containing protein
  • LSU-1
  • LSU-10
  • LSU-11
  • LSU-12
  • LSU-13
  • LSU-14
  • LSU-15
  • LSU-16
  • LSU-17
  • LSU-18
  • LSU-19
  • LSU-2
  • LSU-20
  • LSU-21
  • LSU-22
  • LSU-23
  • LSU-24
  • LSU-25
  • LSU-26
  • LSU-27
  • LSU-28
  • LSU-29
  • LSU-3
  • LSU-30
  • LSU-31
  • LSU-4
  • LSU-5
  • LSU-6
  • LSU-7
  • LSU-8
  • LSU-9
  • Macro domain-containing protein
  • Peptidyl-prolyl cis-trans isomerase
  • Putative 60S ribosomal protein L27
  • RNA recognition motif-containing protein
  • RRM domain-containing protein
  • Ribosomal L22p/L17e protein
  • bL27m
  • bL32m
  • bL35m
  • bL36m
  • mL102
  • mL130
  • mL132
  • mL144
  • mL146
  • mL148
  • mL149
  • mL152
  • mL153
  • mL155
  • mL156
  • mL157
  • mL158
  • mL159
  • mL160
  • mL161
  • mL40
  • mL53
KeywordsRIBOSOME / Toxoplasma gondii / parasite / mitochondrial ribosome / LSU / large subunit
Function / homology
Function and homology information


regulation of mitochondrial mRNA stability / ribonucleoprotein granule / mitochondrial RNA processing / mitochondrial large ribosomal subunit / mitochondrial translation / cyclosporin A binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / ubiquitin-protein transferase activity ...regulation of mitochondrial mRNA stability / ribonucleoprotein granule / mitochondrial RNA processing / mitochondrial large ribosomal subunit / mitochondrial translation / cyclosporin A binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / ubiquitin-protein transferase activity / protein folding / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / DNA-binding transcription factor activity / ribonucleoprotein complex / mRNA binding / DNA binding / RNA binding / nucleus / membrane / cytoplasm
Similarity search - Function
HECTD4 / : / Domain of unknown function (DUF6831) / Domain of unknown function (DUF6832) / RAP domain / RAP domain / RAP domain profile. / RAP / AP2 domain / AP2/ERF domain ...HECTD4 / : / Domain of unknown function (DUF6831) / Domain of unknown function (DUF6832) / RAP domain / RAP domain / RAP domain profile. / RAP / AP2 domain / AP2/ERF domain / : / FAS1 domain / FAS1 domain superfamily / : / FAS1/BIgH3 domain profile. / Ribosomal protein L37, mitochondrial / Mitochondrial ribosomal protein L37 / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / 39S ribosomal protein L46, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / : / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / RNA recognition motif / RNA recognition motif / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Ribosomal protein L9/RNase H1, N-terminal / RNA-binding domain superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / L28p-like / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L24 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L2, domain 3 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / RNA / RNA (> 10) / RNA (> 100) / Ribosomal protein L9, N-terminal domain-containing protein / Uncharacterized protein / Large ribosomal subunit protein uL4m / RAP domain-containing protein / Large ribosomal subunit protein uL3m / Uncharacterized protein ...FE2/S2 (INORGANIC) CLUSTER / RNA / RNA (> 10) / RNA (> 100) / Ribosomal protein L9, N-terminal domain-containing protein / Uncharacterized protein / Large ribosomal subunit protein uL4m / RAP domain-containing protein / Large ribosomal subunit protein uL3m / Uncharacterized protein / Ribosomal protein RPL22 / Large ribosomal subunit protein mL49 / Uncharacterized protein / Uncharacterized protein / Putative 50S ribosomal protein L33 / Ribosomal protein L46 / Uncharacterized protein / Large ribosomal subunit protein uL24c / Ribosomal l25 family protein / Uncharacterized protein / Uncharacterized protein / Putative 60S ribosomal protein L27 / 50S ribosomal protein L19, chloroplastic / Uncharacterized protein / RAP domain-containing protein / Uncharacterized protein / BIR protein / Putative 50S ribosomal protein L13 / Uncharacterized protein / Putative ribosomal protein L28 / Putative LSU ribosomal protein L14P / Large ribosomal subunit protein uL29m / Uncharacterized protein / AP2 domain transcription factor AP2VIIb-2 / Large ribosomal subunit protein uL23m / RAP domain-containing protein / RAP domain-containing protein / Macro domain-containing protein / Uncharacterized protein / Transmembrane protein / HECT-domain (Ubiquitin-transferase) domain-containing protein / Large ribosomal subunit protein bL21m / Putative 50S ribosomal protein L16 / Large ribosomal subunit protein uL24c / Uncharacterized protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / RAP domain-containing protein / RAP domain-containing protein / Transmembrane protein / FAS1 domain-containing protein / DUF6832 domain-containing protein / Large ribosomal subunit protein mL43 / Uncharacterized protein / Uncharacterized protein / AP2 domain transcription factor AP2IV-1 / Putative ribosomal protein L11 / Uncharacterized protein / Putative LSU ribosomal protein L2P / Putative 50S ribosomal protein L17 / RAP domain-containing protein / RNA recognition motif-containing protein / Putative ribosomal protein L20 / Uncharacterized protein / Uncharacterized protein / RRM domain-containing protein / Ribosomal l25 family protein / Ribosomal L22p/L17e protein / Large ribosomal subunit protein mL54 / Ribosomal protein L15, putative / Uncharacterized protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsTobiasson, V. / Shikha, S. / Muhleip, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Numerous rRNA molecules form the apicomplexan mitoribosome via repurposed protein and RNA elements.
Authors: Shikha Shikha / Victor Tobiasson / Mariana Ferreira Silva / Jana Ovciarikova / Dario Beraldi / Alexander Mühleip / Lilach Sheiner /
Abstract: Mitochondrial ribosomes (mitoribosomes) are essential, and their function of synthesising mitochondrial proteins is universal. The core of almost all mitoribosomes is formed from a small number of ...Mitochondrial ribosomes (mitoribosomes) are essential, and their function of synthesising mitochondrial proteins is universal. The core of almost all mitoribosomes is formed from a small number of long and self-folding rRNA molecules. In contrast, the mitoribosome of the apicomplexan parasite Toxoplasma gondii assembles from over 50 extremely short rRNA molecules. Here, we use cryo-EM to discover the features that enable this unusual mitoribosome to perform its function. We reveal that poly-A tails added to rRNA molecules are integrated into the ribosome, and we demonstrate their essentiality for mitoribosome formation and for parasite survival. This is a distinct function for poly-A tails, which are otherwise known primarily as stabilisers of messenger RNAs. Furthermore, while ribosomes typically consist of unique rRNA sequences, here nine sequences are used twice, each copy integrated in a different mitoribosome domain, revealing one of the mechanisms enabling the extreme mitochondrial genome reduction characteristic to Apicomplexa and to a large group of related microbial eukaryotes. Finally, several transcription factor-like proteins are repurposed to compensate for reduced or lost critical ribosomal domains, including members of the ApiAP2 family thus far considered to be DNA-binding transcription factors.
History
DepositionJan 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Aa: Putative LSU ribosomal protein L2P
Ab: Large ribosomal subunit protein uL3m
Ac: Large ribosomal subunit protein uL4m
Ad: HECT-domain (Ubiquitin-transferase) domain-containing protein
Ae: Ribosomal protein L9, N-terminal domain-containing protein
Af: Putative ribosomal protein L11
Ag: Putative 50S ribosomal protein L13
Ah: Putative LSU ribosomal protein L14P
Ai: Ribosomal protein L15, putative
Aj: Putative 50S ribosomal protein L16
Ak: Putative 50S ribosomal protein L17
Al: 50S ribosomal protein L19, chloroplastic
Am: Putative ribosomal protein L20
An: Large ribosomal subunit protein bL21m
Ao: Ribosomal L22p/L17e protein
Ap: Large ribosomal subunit protein uL23m
Aq: Large ribosomal subunit protein uL24c
Ar: Ribosomal l25 family protein
As: bL27m
At: Putative ribosomal protein L28
Au: Large ribosomal subunit protein uL29m
Av: bL32m
Aw: Putative 50S ribosomal protein L33
Ax: bL35m
Ay: bL36m
Az: mL40
AA: Putative 60S ribosomal protein L27
AB: Large ribosomal subunit protein mL43
AC: Ribosomal protein L46
AD: Large ribosomal subunit protein mL49
AE: mL53
AF: Large ribosomal subunit protein mL54
AG: BIR protein
AH: mL102
AI: RAP domain-containing protein
Xa: mL130
Xb: RRM domain-containing protein
Xc: mL132
Xd: RAP domain-containing protein
Xe: Large ribosomal subunit protein uL24c
Xf: FAS1 domain-containing protein
Xg: DUF6832 domain-containing protein
Xh: RAP domain-containing protein
Xi: RAP domain-containing protein
Xj: RAP domain-containing protein
Xk: RNA recognition motif-containing protein
Xl: RAP domain-containing protein
Xm: Macro domain-containing protein
Xn: AP2 domain transcription factor AP2VIIb-2
Xo: mL144
Xp: Peptidyl-prolyl cis-trans isomerase
Xq: mL146
Xr: RAP domain-containing protein
Xs: mL149
Xt: mL148
Xv: RAP domain-containing protein
Xw: Transmembrane protein
Xx: mL152
Xy: mL153
Xz: AP2 domain transcription factor AP2IV-1
XA: mL155
XB: mL156
XC: mL157
XD: mL158
XE: mL159
XF: mL160
XG: mL161
XH: Ribosomal protein RPL22
XI: Transmembrane protein
XJ: Chain Ua
Ua: Ribosomal l25 family protein
Ub: Chain Uc
Uc: Chain Ud
Ud: Chain Ue
Ue: Chain Uf
Uf: LSU-1
RA: LSU-2
RB: LSU-3
RC: LSU-4
RD: LSU-5
RE: LSU-6
RF: LSU-7
RG: LSU-8
RI: LSU-9
RJ: LSU-10
RK: LSU-11
RL: LSU-12
RM: LSU-13
RN: LSU-14
RO: LSU-15
RP: LSU-16
RQ: LSU-17
RS: LSU-18
RT: LSU-19
RU: LSU-20
RV: LSU-21
RW: LSU-22
RX: LSU-23
RY: LSU-24
RZ: LSU-25
Ra: LSU-26
Rb: LSU-27
Rc: LSU-28
Rd: LSU-29
Rf: LSU-30
Rg: LSU-31
Rh: LSU-32
Ri: LSU-32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,935,328111
Polymers3,934,911108
Non-polymers4173
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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Putative LSU ribosomal protein ... , 2 types, 2 molecules AaAh

#1: Protein Putative LSU ribosomal protein L2P


Mass: 62157.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KET1
#8: Protein Putative LSU ribosomal protein L14P


Mass: 13986.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K196

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Large ribosomal subunit protein ... , 10 types, 10 molecules AbAcAnApAqAuABADAFXe

#2: Protein Large ribosomal subunit protein uL3m


Mass: 56206.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A2G8Y818
#3: Protein Large ribosomal subunit protein uL4m


Mass: 91060.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A151HQQ9
#14: Protein Large ribosomal subunit protein bL21m


Mass: 77440.164 Da / Num. of mol.: 1 / Mutation: A400Q, A405R / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K7U7
#16: Protein Large ribosomal subunit protein uL23m


Mass: 29216.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K299
#17: Protein Large ribosomal subunit protein uL24c


Mass: 48147.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JXG2
#21: Protein Large ribosomal subunit protein uL29m


Mass: 28367.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K1F8
#28: Protein Large ribosomal subunit protein mL43


Mass: 23624.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KC95
#30: Protein Large ribosomal subunit protein mL49


Mass: 33466.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JUD4
#32: Protein Large ribosomal subunit protein mL54


Mass: 55962.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F6A8
#40: Protein Large ribosomal subunit protein uL24c


Mass: 25957.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K981

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Protein , 34 types, 34 molecules AdAlAoAsAvAxAyAzAAAEAGAHXaXbXcXfXgXkXmXoXpXqXsXtXxXyXAXBXCXD...

#4: Protein HECT-domain (Ubiquitin-transferase) domain-containing protein


Mass: 43075.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K7T4
#12: Protein 50S ribosomal protein L19, chloroplastic


Mass: 84072.586 Da / Num. of mol.: 1 / Mutation: Y671Q, Y674W / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JZ22
#15: Protein Ribosomal L22p/L17e protein


Mass: 64822.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8F1I2
#19: Protein bL27m


Mass: 43964.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GME4
#22: Protein bL32m


Mass: 10625.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K9L3
#24: Protein bL35m


Mass: 39434.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KEG8
#25: Protein bL36m


Mass: 22554.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A3R8AVZ6
#26: Protein mL40


Mass: 32801.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KCG7
#27: Protein Putative 60S ribosomal protein L27


Mass: 10721.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JYF7
#31: Protein mL53


Mass: 24687.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JX69
#33: Protein BIR protein


Mass: 32555.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K0B0
#34: Protein mL102


Mass: 43522.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A0F7V869
#36: Protein mL130


Mass: 59500.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JZ23
#37: Protein RRM domain-containing protein


Mass: 75105.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S7UYV0
#38: Protein mL132


Mass: 22764.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JXX9
#41: Protein FAS1 domain-containing protein


Mass: 76075.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KB94
#42: Protein DUF6832 domain-containing protein


Mass: 56097.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_010990 / Production host: Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KC93
#46: Protein RNA recognition motif-containing protein


Mass: 27595.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KGH2
#48: Protein Macro domain-containing protein


Mass: 68141.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K515
#50: Protein mL144


Mass: 103327.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#51: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 31893.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K9Z8, peptidylprolyl isomerase
#52: Protein mL146


Mass: 121147.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K1X6
#54: Protein mL149


Mass: 54289.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JXX4
#55: Protein mL148


Mass: 14034.347 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JV70
#57: Protein mL152


Mass: 31789.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K0Y0
#58: Protein mL153


Mass: 48035.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: Q1JTA3
#60: Protein mL155


Mass: 34626.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KDX2
#61: Protein mL156


Mass: 22703.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K9K6
#62: Protein mL157


Mass: 34078.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JWE1
#63: Protein mL158


Mass: 26651.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S7UHA3
#64: Protein mL159


Mass: 17303.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KA70
#65: Protein mL160


Mass: 16011.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JZI4
#66: Protein mL161


Mass: 51870.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K5D7
#69: Protein Chain Ua


Mass: 30943.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)

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Ribosomal protein ... , 4 types, 4 molecules AeAiACXH

#5: Protein Ribosomal protein L9, N-terminal domain-containing protein


Mass: 54036.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A086JV44
#9: Protein Ribosomal protein L15, putative


Mass: 71016.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8GIU7
#29: Protein Ribosomal protein L46


Mass: 67516.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JX23
#67: Protein Ribosomal protein RPL22


Mass: 38201.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JUA9

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Putative ribosomal protein ... , 3 types, 3 molecules AfAmAt

#6: Protein Putative ribosomal protein L11


Mass: 20103.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KEF6
#13: Protein Putative ribosomal protein L20


Mass: 14574.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PY19
#20: Protein Putative ribosomal protein L28


Mass: 33345.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K129

+
Putative 50S ribosomal protein ... , 4 types, 4 molecules AgAjAkAw

#7: Protein Putative 50S ribosomal protein L13


Mass: 26050.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K0U2
#10: Protein Putative 50S ribosomal protein L16


Mass: 21351.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K7Z7
#11: Protein Putative 50S ribosomal protein L17


Mass: 29333.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KEY9
#23: Protein Putative 50S ribosomal protein L33


Mass: 15185.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JWI3

+
Ribosomal l25 family ... , 2 types, 2 molecules ArUa

#18: Protein Ribosomal l25 family protein


Mass: 80776.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S8ER88
#70: Protein/peptide Ribosomal l25 family protein


Mass: 2842.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JXW0

+
RAP domain-containing ... , 7 types, 8 molecules AIXdXhXiXjXlXvXr

#35: Protein RAP domain-containing protein


Mass: 73547.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KFM0
#39: Protein RAP domain-containing protein


Mass: 98356.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A2G8XP01
#43: Protein RAP domain-containing protein


Mass: 69902.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KAP7
#44: Protein RAP domain-containing protein


Mass: 51921.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K2J1
#45: Protein RAP domain-containing protein


Mass: 113716.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K4L1
#47: Protein RAP domain-containing protein


Mass: 72010.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JZB1
#53: Protein RAP domain-containing protein


Mass: 78688.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KAD2

+
AP2 domain transcription factor ... , 2 types, 2 molecules XnXz

#49: Protein AP2 domain transcription factor AP2VIIb-2


Mass: 62047.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K291
#59: Protein AP2 domain transcription factor AP2IV-1


Mass: 47659.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KEE5

+
Transmembrane ... , 2 types, 2 molecules XwXI

#56: Protein Transmembrane protein


Mass: 36669.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KAS3
#68: Protein Transmembrane protein


Mass: 22652.986 Da / Num. of mol.: 1 / Mutation: Q239S, P236S / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K730

+
Protein/peptide , 5 types, 5 molecules UbUcUdUeUf

#71: Protein/peptide Chain Uc


Mass: 2501.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#72: Protein/peptide Chain Ud


Mass: 1708.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#73: Protein/peptide Chain Ue


Mass: 3149.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#74: Protein/peptide Chain Uf


Mass: 1462.696 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#75: Protein/peptide LSU-1


Mass: 528.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)

+
RNA chain , 32 types, 32 molecules RARBRCRDRERFRGRIRJRKRLRMRNRORPRQRSRTRURVRWRXRYRZRaRbRcRdRfRgRhRi

#76: RNA chain LSU-2


Mass: 11145.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#77: RNA chain LSU-3


Mass: 8744.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#78: RNA chain LSU-4


Mass: 10680.544 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#79: RNA chain LSU-5


Mass: 29383.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#80: RNA chain LSU-6


Mass: 14103.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#81: RNA chain LSU-7


Mass: 9490.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#82: RNA chain LSU-8


Mass: 26913.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#83: RNA chain LSU-9


Mass: 11693.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#84: RNA chain LSU-10


Mass: 18880.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#85: RNA chain LSU-11


Mass: 3239.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#86: RNA chain LSU-12


Mass: 57332.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#87: RNA chain LSU-13


Mass: 22879.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#88: RNA chain LSU-14


Mass: 8288.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#89: RNA chain LSU-15


Mass: 8406.138 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#90: RNA chain LSU-16


Mass: 3656.306 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#91: RNA chain LSU-17


Mass: 21973.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#92: RNA chain LSU-18


Mass: 30072.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#93: RNA chain LSU-19


Mass: 9120.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#94: RNA chain LSU-20


Mass: 4863.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#95: RNA chain LSU-21


Mass: 11298.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#96: RNA chain LSU-22


Mass: 29090.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#97: RNA chain LSU-23


Mass: 88940.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#98: RNA chain LSU-24


Mass: 15299.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#99: RNA chain LSU-25


Mass: 14644.009 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#100: RNA chain LSU-26


Mass: 16123.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#101: RNA chain LSU-27


Mass: 8935.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#102: RNA chain LSU-28


Mass: 64666.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#103: RNA chain LSU-29


Mass: 25808.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#104: RNA chain LSU-30


Mass: 9449.827 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#105: RNA chain LSU-31


Mass: 4518.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#106: RNA chain LSU-32


Mass: 15828.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#107: RNA chain LSU-32


Mass: 14152.343 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)

+
Non-polymers , 2 types, 3 molecules

#108: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#109: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2

+
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: mitochondrial ribososome from Toxoplasma gondii / Type: RIBOSOME / Entity ID: #1-#106 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Toxoplasma gondii (eukaryote) / Strain: RH
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.21rc1_5058: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 375745 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002179537
ELECTRON MICROSCOPYf_angle_d0.582252071
ELECTRON MICROSCOPYf_dihedral_angle_d11.83541306
ELECTRON MICROSCOPYf_chiral_restr0.09828871
ELECTRON MICROSCOPYf_plane_restr0.00525148

+
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