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- PDB-9hqv: Cryo-EM structure of the small subunit of the mitochondrial ribos... -

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Entry
Database: PDB / ID: 9hqv
TitleCryo-EM structure of the small subunit of the mitochondrial ribosome from Toxoplasma gondii
Components
  • (Mitochondrial ...) x 2
  • (Putative 30S ribosomal protein ...) x 4
  • (Putative ribosomal protein ...) x 6
  • (RAP domain-containing ...) x 2
  • (Ribosomal protein, ...) x 2
  • (Small ribosomal subunit protein ...) x 2
  • AP2 domain transcription factor AP2IX-6
  • ARG-ALA-GLU-LEU-VAL-ALA-ALA-GLN-VAL-ARG-GLU-LYS-LEU-ALA-ILE-LYS-MET-ALA-ASN-ALA-LEU-ALA
  • ATP-dependent Clp protease proteolytic subunit,related protein
  • Acylphosphatase-like domain-containing protein
  • CHCH domain-containing protein
  • Chain UC
  • Chain Uh
  • Chain Uj
  • Chain Un
  • DNA double-strand break repair rad50 ATPase
  • DnaJ domain-containing protein
  • Enoyl-CoA hydratase/isomerase family protein
  • GLY-ARG-SER-LYS-VAL-LEU-ILE-ARG-ARG-LEU-LYS-GLU-ARG-ALA-LYS-LYS-GLU-ALA-GLU-LYS-LYS-ALA
  • Homeodomain-like containing protein
  • Macro domain-containing protein
  • Pentatricopeptide repeat domain-containing protein
  • Putative mitochondrial ribosomal protein s6-2
  • SSU-1
  • SSU-10
  • SSU-11
  • SSU-12
  • SSU-13
  • SSU-14
  • SSU-15
  • SSU-16
  • SSU-17
  • SSU-18
  • SSU-19
  • SSU-2
  • SSU-20
  • SSU-21
  • SSU-3
  • SSU-4
  • SSU-5
  • SSU-6
  • SSU-7
  • SSU-8
  • SSU-9
  • Thioredoxin domain-containing protein
  • UNK1
  • UNK2
  • UNK3
  • UNK4
  • Unknown peptide
  • chain Uo
  • chain Up
  • chain Uq
  • mS117
  • mS119
  • mS120
  • mS121
  • mS124
  • mS125
  • mS128
  • mS131
  • mS132
  • mS133
  • mS135
  • mS136
  • mS137
  • mS138
  • mS23
  • mS34
  • mS45
  • mS75
  • mS92
  • tRNA E-site
  • uS10m
  • us13m
KeywordsRIBOSOME / Toxoplasma gondii / parasite / mitochondrial ribosome / SSU / large subunit
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 / RNA binding / membrane / cytoplasm
Similarity search - Function
: / Apicomplexa microprotein / : / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Ribosomal protein S23/S29, mitochondrial ...: / Apicomplexa microprotein / : / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S9 / Ribosomal protein S9/S16 / 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
ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Mitochondrial mRNA-processing protein COX24 C-terminal domain-containing protein / Putative ribosomal protein S17 / Acylphosphatase-like domain-containing protein / Putative 30S ribosomal protein S12 / Putative ribosomal protein S14 ...ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Mitochondrial mRNA-processing protein COX24 C-terminal domain-containing protein / Putative ribosomal protein S17 / Acylphosphatase-like domain-containing protein / Putative 30S ribosomal protein S12 / Putative ribosomal protein S14 / Small ribosomal subunit protein mS29 / CHCH domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Putative 30S ribosomal protein S15 / Uncharacterized protein / DNA double-strand break repair rad50 ATPase / Uncharacterized protein / Putative ribosomal protein S8 / ATP-dependent Clp protease proteolytic subunit,related protein / Thioredoxin domain-containing protein / Uncharacterized protein / Uncharacterized protein / Putative ribosomal protein S11 / Uncharacterized protein / Uncharacterized protein / Macro domain-containing protein / Uncharacterized protein / Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein / RAP domain-containing protein / Uncharacterized protein / Putative mitochondrial ribosomal protein s6-2 / Homeodomain-like containing protein / Putative 30S ribosomal protein S5 / DnaJ domain-containing protein / Uncharacterized protein / Uncharacterized protein / Putative 30S ribosomal protein S16 / AP2 domain transcription factor AP2IX-6 / Pentatricopeptide repeat domain-containing protein / Uncharacterized protein / Uncharacterized protein / Putative ribosomal protein S9 / Uncharacterized protein / Enoyl-CoA hydratase/isomerase family protein / RAP domain-containing protein / Uncharacterized protein / Uncharacterized protein / Putative ribosomal protein S18 / Uncharacterized protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.52 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
DepositionDec 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
BA: Enoyl-CoA hydratase/isomerase family protein
BB: mS75
BC: Pentatricopeptide repeat domain-containing protein
BD: mS92
Ba: Ribosomal protein, uS2m
Bb: Putative 30S ribosomal protein S5
Bc: Putative mitochondrial ribosomal protein s6-2
Bd: Putative ribosomal protein S8
Be: Putative ribosomal protein S9
Bf: uS10m
Bg: Putative ribosomal protein S11
Bh: Putative 30S ribosomal protein S12
Bi: us13m
Bj: Putative ribosomal protein S14
Bk: Putative 30S ribosomal protein S15
Bl: Putative 30S ribosomal protein S16
Bm: Putative ribosomal protein S17
Bn: Putative ribosomal protein S18
Bo: Ribosomal protein, bS21m
Bp: mS23
Bq: Mitochondrial ribosomal protein, mS26
Br: Small ribosomal subunit protein mS29
Bs: DNA double-strand break repair rad50 ATPase
Bt: mS34
Bu: Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein
Bv: CHCH domain-containing protein
Bx: Mitochondrial mRNA-processing protein COX24 C-terminal domain-containing protein
By: Homeodomain-like containing protein
Bz: mS45
Ua: UNK1
Ub: UNK2
Uc: UNK3
Ud: UNK4
Uh: Chain Uh
Ui: Unknown peptide
Uj: Chain Uj
Uk: Unknown peptide
Ul: GLY-ARG-SER-LYS-VAL-LEU-ILE-ARG-ARG-LEU-LYS-GLU-ARG-ALA-LYS-LYS-GLU-ALA-GLU-LYS-LYS-ALA
Um: ARG-ALA-GLU-LEU-VAL-ALA-ALA-GLN-VAL-ARG-GLU-LYS-LEU-ALA-ILE-LYS-MET-ALA-ASN-ALA-LEU-ALA
Un: Chain Un
Uo: chain Uo
Up: chain Up
Uq: chain Uq
Ya: mS117
Yb: ATP-dependent Clp protease proteolytic subunit,related protein
Yc: mS119
Yd: mS120
Ye: mS121
Yf: Macro domain-containing protein
Yg: Thioredoxin domain-containing protein
Yh: mS124
Yi: mS125
Yj: DnaJ domain-containing protein
Yk: RAP domain-containing protein
Yl: mS128
Ym: RAP domain-containing protein
Yn: AP2 domain transcription factor AP2IX-6
Yo: mS131
Yp: mS132
Yr: Acylphosphatase-like domain-containing protein
Ys: mS135
Yt: mS136
Yu: mS137
Yq: mS133
SA: SSU-1
SB: SSU-2
SC: SSU-3
SD: SSU-4
SE: SSU-5
SF: SSU-6
SG: SSU-7
SH: SSU-8
SI: SSU-9
SJ: SSU-10
SK: SSU-11
SL: SSU-12
SM: SSU-13
SN: SSU-14
SO: SSU-15
SP: SSU-16
SQ: SSU-17
SR: SSU-18
SS: SSU-19
ST: SSU-20
SU: SSU-21
TP: tRNA E-site
UC: Chain UC
Yv: mS138
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,927,67291
Polymers2,927,07588
Non-polymers5973
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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Protein , 35 types, 35 molecules BABCBDBcBfBiBpBsBtBvByBzUdUhUjYaYbYcYdYeYfYgYhYiYjYlYnYoYpYr...

#1: 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
#3: Protein Pentatricopeptide repeat domain-containing protein


Mass: 74866.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KDF6
#4: Protein mS92


Mass: 17313.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KCE0
#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 uS10m


Mass: 26919.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K2E1
#13: Protein us13m


Mass: 12679.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KC71
#20: Protein mS23


Mass: 41599.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K2Y2
#23: Protein DNA double-strand break repair rad50 ATPase


Mass: 69085.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K0I6
#24: Protein mS34


Mass: 34184.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JYF4
#26: 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
#28: Protein Homeodomain-like containing protein


Mass: 66947.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KAD0
#29: Protein mS45


Mass: 59593.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JZ68
#33: Protein UNK4


Mass: 6384.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#34: Protein Chain Uh


Mass: 5997.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#36: Protein Chain Uj


Mass: 5124.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#43: Protein mS117


Mass: 60305.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S7V2J1
#44: Protein ATP-dependent Clp protease proteolytic subunit,related protein


Mass: 116313.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K1B3
#45: Protein mS119


Mass: 28744.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KFI1
#46: Protein mS120


Mass: 75017.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K8Y5
#47: Protein mS121


Mass: 34469.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JZ58
#48: Protein Macro domain-containing protein


Mass: 75947.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K475
#49: Protein Thioredoxin domain-containing protein


Mass: 102709.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K257
#50: Protein mS124


Mass: 30802.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#51: Protein mS125


Mass: 100897.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JYP0
#52: 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
#54: Protein mS128


Mass: 34440.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KEX1
#56: Protein AP2 domain transcription factor AP2IX-6


Mass: 47928.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KDC3
#57: Protein mS131


Mass: 48451.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KFW2
#58: Protein mS132


Mass: 19356.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K2N1
#59: Protein Acylphosphatase-like domain-containing protein


Mass: 27403.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YXT0
#60: Protein mS135


Mass: 21353.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K0G8
#61: Protein mS136


Mass: 50588.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K0Z5
#62: Protein mS137


Mass: 40441.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#63: Protein mS133


Mass: 31971.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PYD6
#87: Protein mS138


Mass: 44338.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K328

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Protein/peptide , 11 types, 12 molecules BBUaUbUcUiUkUlUmUnUoUpUq

#2: Protein/peptide mS75


Mass: 3196.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#30: Protein/peptide UNK1


Mass: 1720.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#31: Protein/peptide UNK2


Mass: 541.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#32: Protein/peptide UNK3


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


Mass: 1124.378 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#37: Protein/peptide GLY-ARG-SER-LYS-VAL-LEU-ILE-ARG-ARG-LEU-LYS-GLU-ARG-ALA-LYS-LYS-GLU-ALA-GLU-LYS-LYS-ALA


Mass: 2605.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#38: Protein/peptide ARG-ALA-GLU-LEU-VAL-ALA-ALA-GLN-VAL-ARG-GLU-LYS-LEU-ALA-ILE-LYS-MET-ALA-ASN-ALA-LEU-ALA


Mass: 2370.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#39: Protein/peptide Chain Un


Mass: 2785.136 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#40: Protein/peptide chain Uo


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


Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#42: Protein/peptide chain Uq


Mass: 2842.475 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 BaBo

#5: 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
#19: 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

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Putative 30S ribosomal protein ... , 4 types, 4 molecules BbBhBkBl

#6: Protein Putative 30S ribosomal protein S5


Mass: 127355.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KBH4
#12: Protein Putative 30S ribosomal protein S12


Mass: 66403.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JTW0
#15: 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
#16: 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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Putative ribosomal protein ... , 6 types, 6 molecules BdBeBgBjBmBn

#8: 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
#9: Protein Putative ribosomal protein S9


Mass: 57283.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KFS1
#11: Protein Putative ribosomal protein S11


Mass: 43478.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K2Q1
#14: Protein Putative ribosomal protein S14


Mass: 13063.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JW76
#17: 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
#18: Protein Putative ribosomal protein S18


Mass: 84433.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S7VTU6

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Mitochondrial ... , 2 types, 2 molecules BqBx

#21: 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
#27: Protein Mitochondrial mRNA-processing protein COX24 C-terminal domain-containing protein


Mass: 30027.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A0F7UNZ9

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Small ribosomal subunit protein ... , 2 types, 2 molecules BrBu

#22: Protein Small ribosomal subunit protein mS29


Mass: 63068.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6JWV4
#25: Protein Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein


Mass: 63908.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K5S5

+
RAP domain-containing ... , 2 types, 2 molecules YkYm

#53: Protein RAP domain-containing protein


Mass: 168668.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6KGV4
#55: Protein RAP domain-containing protein


Mass: 86967.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A7J6K7K5

+
RNA chain , 23 types, 23 molecules SASBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUTPUC

#64: RNA chain SSU-1


Mass: 29088.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#65: RNA chain SSU-2


Mass: 9185.558 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#66: RNA chain SSU-3


Mass: 7468.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#67: RNA chain SSU-4


Mass: 15105.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#68: RNA chain SSU-5


Mass: 23627.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#69: RNA chain SSU-6


Mass: 38630.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#70: RNA chain SSU-7


Mass: 8277.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#71: RNA chain SSU-8


Mass: 8141.964 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#72: RNA chain SSU-9


Mass: 17142.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#73: RNA chain SSU-10


Mass: 29992.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#74: RNA chain SSU-11


Mass: 36511.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#75: RNA chain SSU-12


Mass: 8951.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#76: RNA chain SSU-13


Mass: 23947.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#77: RNA chain SSU-14


Mass: 7857.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#78: RNA chain SSU-15


Mass: 5098.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#79: RNA chain SSU-16


Mass: 10632.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#80: RNA chain SSU-17


Mass: 18121.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#81: RNA chain SSU-18


Mass: 10786.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#82: RNA chain SSU-19


Mass: 3811.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#83: RNA chain SSU-20


Mass: 7859.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#84: RNA chain SSU-21


Mass: 17588.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#85: RNA chain tRNA E-site


Mass: 6715.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#86: RNA chain Chain UC


Mass: 9971.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)

+
Non-polymers , 3 types, 3 molecules

#88: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#89: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#90: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

+
Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

-
Sample preparation

ComponentName: mitochondrial small ribosomal subunit from Toxoplasma gondii
Type: RIBOSOME / Entity ID: #1-#87 / 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 R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen 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 / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 70 K
Image recordingElectron dose: 36 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
2PHENIX1.21rc1_5058:model refinement
134.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 375745 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002133649
ELECTRON MICROSCOPYf_angle_d0.439185946
ELECTRON MICROSCOPYf_dihedral_angle_d12.46453840
ELECTRON MICROSCOPYf_chiral_restr0.03421148
ELECTRON MICROSCOPYf_plane_restr0.00419931

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