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- PDB-6z1p: Structure of the mitochondrial ribosome from Tetrahymena thermophila -

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Basic information

Entry
Database: PDB / ID: 6z1p
TitleStructure of the mitochondrial ribosome from Tetrahymena thermophila
Components
  • (30S ribosomal protein ...) x 4
  • (50S ribosomal protein ...) x 9
  • (Ribosomal protein ...) x 20
  • (bL7/12m) x 2
  • 39-S ribosomal protein L47
  • Enoyl-CoA hydratase/isomerase
  • IGR motif protein
  • Iron donor protein CyaY
  • Iron-binding zinc finger CDGSH type protein
  • LSU rRNA_1
  • LSU rRNA_2
  • Large subunit ribosomal protein
  • PARP alpha-helical domain-containing protein,mS83
  • Ribosomal death-associated protein
  • Ribosomal protein
  • Ribosomal subunit protein
  • SSU rRNA_1
  • SSU rRNA_2
  • SelR domain protein
  • Signal peptide-binding domain protein
  • Ymf59
  • Ymf60
  • Ymf61
  • Ymf63
  • Ymf64
  • Ymf69
  • Ymf73
  • Ymf74
  • Ymf76
  • bL19m
  • bL25m
  • bL32m
  • bL35m
  • bL7/L12m
  • bS21m
  • mL101
  • mL102
  • mL103
  • mL104
  • mL106
  • mL40
  • mL46
  • mL53
  • mL54
  • mL64
  • mS23
  • mS26
  • mS31
  • mS33
  • mS34
  • mS37
  • mS38
  • mS45
  • mS75
  • mS76
  • mS77
  • mS78
  • mS79
  • mS81
  • mS82
  • mS84,mS84
  • mS85
  • mS87
  • mS88
  • mS89
  • mS90
  • mS91
  • mS93
KeywordsRIBOSOME / Mitochondrial ribosome / mitochondria / ciliate / tetrahymena
Function / homology
Function and homology information


3-hydroxyisobutyryl-CoA hydrolase / peptide-methionine (R)-S-oxide reductase / 3-hydroxyisobutyryl-CoA hydrolase activity / peptide-methionine (R)-S-oxide reductase activity / L-valine catabolic process / iron chaperone activity / signal recognition particle / protein repair / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane ...3-hydroxyisobutyryl-CoA hydrolase / peptide-methionine (R)-S-oxide reductase / 3-hydroxyisobutyryl-CoA hydrolase activity / peptide-methionine (R)-S-oxide reductase activity / L-valine catabolic process / iron chaperone activity / signal recognition particle / protein repair / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / iron-sulfur cluster assembly / ferroxidase activity / NAD+ poly-ADP-ribosyltransferase activity / ferric iron binding / iron ion transport / ferrous iron binding / 2 iron, 2 sulfur cluster binding / large ribosomal subunit / response to oxidative stress / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / nucleic acid binding / intracellular iron ion homeostasis / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding / metal ion binding / membrane / cytoplasm
Similarity search - Function
: / : / Peptide methionine sulfoxide reductase MsrB / Iron-binding zinc finger CDGSH type / Peptide methionine sulphoxide reductase MrsB domain / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Iron-binding zinc finger, CDGSH type / MitoNEET, CDGSH iron-sulfur domain ...: / : / Peptide methionine sulfoxide reductase MsrB / Iron-binding zinc finger CDGSH type / Peptide methionine sulphoxide reductase MrsB domain / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Iron-binding zinc finger, CDGSH type / MitoNEET, CDGSH iron-sulfur domain / CDGSH-type zinc finger. Function unknown. / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Protein Fyv4 / Mss4-like superfamily / Small ribosomal subunit protein mS41 SAM domain / Transcription termination factor, mitochondrial/chloroplastic / IGR protein motif / MTERF superfamily, mitochondrial/chloroplastic / mTERF / IGR / Frataxin/CyaY superfamily / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / Ribosomal protein L37, mitochondrial / Mitochondrial ribosomal protein L37 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / : / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / ClpP/crotonase-like domain superfamily / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L9, C-terminal domain superfamily / 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 L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / RNA-binding domain superfamily / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / 50S ribosomal protein L17 / Uncharacterized protein ...ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / 50S ribosomal protein L17 / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein bL28m / mTERF protein / Large ribosomal subunit protein bL21m / Uncharacterized protein / Uncharacterized protein / 39S ribosomal protein L46, mitochondrial / Uncharacterized protein / 50S ribosomal protein L27 / Uncharacterized protein / Ribosomal protein L19 / 30S ribosomal protein S16 / Uncharacterized protein / Ribosomal protein S9 / 30S ribosomal protein S5 / 30S ribosomal protein S17 / Uncharacterized protein / 50S ribosomal protein L35 / Large ribosomal subunit protein mL49 / Ribosomal protein L15, putative / Ribosomal protein L27 / Large ribosomal subunit protein uL4m / Ribosomal protein S6 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein uL23m / Small ribosomal subunit protein mS41 / EF-hand domain-containing protein / Iron-binding zinc finger CDGSH type protein / Large ribosomal subunit protein uL3m / Uncharacterized protein / 50S ribosomal protein L33 / PARP alpha-helical domain-containing protein / 3-hydroxyisobutyryl-CoA hydrolase / Large ribosomal subunit protein mL43 / Small ribosomal subunit protein mS29 / RRM domain-containing protein / Large ribosomal subunit protein uL29m / peptide-methionine (R)-S-oxide reductase / 30S ribosomal protein S15 / 50S ribosomal protein L20 / Ribosomal protein L22/L17e / Uncharacterized protein / Uncharacterized protein / Ribosomal subunit protein / Ribosomal protein S18 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Iron donor protein CyaY / Ribosomal protein L9, amine-terminal domain protein / Large ribosomal subunit protein uL24c / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein L7/L12 carboxy-terminal domain protein / Ymf73 / Ribosomal protein L14 / Ymf61 / Ribosomal protein L16 / Ymf59 / Ymf69 / Ymf63 / Ymf64 / Ymf60 / Ribosomal protein S14 / Ribosomal protein S12 / Ymf74 / Ribosomal protein L2 / Ribosomal protein S19 / Ribosomal protein S3 / Ribosomal protein S13 / Ymf76 / Uncharacterized protein / 50S ribosomal protein L13 / Signal peptide-binding domain protein / Ribosomal protein / Ribosomal protein L11, amine-terminal domain protein
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsTobiasson, V. / Amunts, A.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
Knut and Alice Wallenberg Foundation2018.0080
CitationJournal: Elife / Year: 2020
Title: Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation.
Authors: Victor Tobiasson / Alexey Amunts /
Abstract: To understand the steps involved in the evolution of translation, we used , a ciliate with high coding capacity of the mitochondrial genome, as the model organism and characterized its mitochondrial ...To understand the steps involved in the evolution of translation, we used , a ciliate with high coding capacity of the mitochondrial genome, as the model organism and characterized its mitochondrial ribosome (mitoribosome) using cryo-EM. The structure of the mitoribosome reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit, while the large subunit lacks 5S rRNA. The structure also shows that the small subunit head is constrained, tRNA binding sites are formed by mitochondria-specific protein elements, conserved protein bS1 is excluded, and bacterial RNA polymerase binding site is blocked. We provide evidence for anintrinsic protein targeting system through visualization of mitochondria-specific mL105 by the exit tunnel that would facilitate the recruitment of a nascent polypeptide. Functional protein uS3m is encoded by three complementary genes from the nucleus and mitochondrion, establishing a link between genetic drift and mitochondrial translation. Finally, we reannotated nine open reading frames in the mitochondrial genome that code for mitoribosomal proteins.
History
DepositionMay 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
Aa: LSU rRNA_1
Ab: LSU rRNA_2
Ac: Ribosomal protein L2
Ad: 50S ribosomal protein L3
Ae: 50S ribosomal protein L4
Af: Ymf69
Ag: Ymf60
Ah: bL7/L12m
Ai: bL7/12m
Aj: bL7/12m
Ak: Ribosomal protein L7/L12 carboxy-terminal domain protein
Al: Ribosomal protein L9, amine-terminal domain protein
Am: Ymf74
An: Ribosomal protein L11, amine-terminal domain protein
Ao: 50S ribosomal protein L13
Ap: Ribosomal protein L14
Aq: Ribosomal protein L15, putative
Ar: Ribosomal protein L16
As: 50S ribosomal protein L17
At: bL19m
Au: 50S ribosomal protein L20
Av: 50S ribosomal protein L21
Aw: Ribosomal protein L22/L17e
Ax: Ribosomal protein L23, putative
Ay: 50S ribosomal protein L24
Az: bL25m
AA: 50S ribosomal protein L27
AB: Ribosomal protein L28
AC: 39-S ribosomal protein L47
AD: bL32m
AE: 50S ribosomal protein L33
AF: bL35m
AG: Ribosomal protein
AH: mL40
AI: Ribosomal protein L27
AJ: Ribosomal protein L51/S25/CI-B8 domain protein
AK: mL46
AL: Large subunit ribosomal protein
AM: mL53
AN: mL54
AO: mL64
AP: mL101
AQ: mL102
AR: mL103
AS: mL104
AT: Signal peptide-binding domain protein
AU: mL106
AV: Iron-binding zinc finger CDGSH type protein
Ba: SSU rRNA_1
Bb: SSU rRNA_2
Bc: Ymf73
Bd: Ymf64
Be: Ymf76
Bf: 30S ribosomal protein S5
Bg: Ribosomal protein S6
Bh: Ymf63
Bi: Ribosomal protein S9
Bj: Ymf59
Bk: Ymf61
Bl: Ribosomal protein S12
Bm: Ribosomal protein S13
Bn: Ribosomal protein S14
Bo: 30S ribosomal protein S15
Bp: 30S ribosomal protein S16
Bq: 30S ribosomal protein S17
Br: Ribosomal protein S18
Bs: Ribosomal protein S19
Bt: bS21m
Bu: mS23
Bv: mS26
Bw: Ribosomal death-associated protein
Bx: mS31
By: mS33
Bz: mS34
BA: Ribosomal subunit protein
BB: mS37
BC: mS38
BD: IGR motif protein
BE: mS45
BF: mS75
BG: mS76
BH: mS77
BI: Enoyl-CoA hydratase/isomerase
BJ: mS78
BK: mS79
BL: SelR domain protein
BM: mS81
BN: mS82
BO: PARP alpha-helical domain-containing protein,mS83
BP: mS84,mS84
BQ: mS85
BR: Iron donor protein CyaY
BS: mS87
BT: mS88
BU: mS89
BV: mS90
BW: mS91
BX: Ribosomal protein S3
BY: mS93
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,578,607497
Polymers4,568,06699
Non-polymers10,542398
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 4 types, 4 molecules AaAbBaBb

#1: RNA chain LSU rRNA_1


Mass: 89365.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: GenBank: 15011465
#2: RNA chain LSU rRNA_2


Mass: 743593.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: GenBank: 15011465
#49: RNA chain SSU rRNA_1


Mass: 62976.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: GenBank: 15011465
#50: RNA chain SSU rRNA_2


Mass: 448294.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: GenBank: 15011465

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Ribosomal protein ... , 20 types, 20 molecules AcAkAlAnApAqArAwAxABAIAJBgBiBlBmBnBrBsBX

#3: Protein Ribosomal protein L2


Mass: 29974.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951B6
#11: Protein Ribosomal protein L7/L12 carboxy-terminal domain protein


Mass: 12385.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q24IM4
#12: Protein Ribosomal protein L9, amine-terminal domain protein


Mass: 26227.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q24C33
#14: Protein Ribosomal protein L11, amine-terminal domain protein


Mass: 17816.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: W7XH77
#16: Protein Ribosomal protein L14


Mass: 13612.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q950Y1
#17: Protein Ribosomal protein L15, putative


Mass: 34669.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7MF78
#18: Protein Ribosomal protein L16


Mass: 17462.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951A0
#23: Protein Ribosomal protein L22/L17e


Mass: 42829.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q23CT9
#24: Protein Ribosomal protein L23, putative


Mass: 16210.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22EY1
#28: Protein Ribosomal protein L28


Mass: 35041.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7LU83
#35: Protein Ribosomal protein L27


Mass: 18506.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7MG40
#36: Protein Ribosomal protein L51/S25/CI-B8 domain protein


Mass: 21158.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22RG0
#55: Protein Ribosomal protein S6


Mass: 15971.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7MHS2
#57: Protein Ribosomal protein S9


Mass: 87307.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7M4A2
#60: Protein Ribosomal protein S12


Mass: 15296.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951B3
#61: Protein Ribosomal protein S13


Mass: 33437.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951B9
#62: Protein Ribosomal protein S14


Mass: 12311.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951B0
#66: Protein Ribosomal protein S18


Mass: 63883.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q23K82
#67: Protein Ribosomal protein S19


Mass: 11624.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951B7
#98: Protein Ribosomal protein S3


Mass: 18509.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951B8

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50S ribosomal protein ... , 9 types, 9 molecules AdAeAoAsAuAvAyAAAE

#4: Protein 50S ribosomal protein L3


Mass: 49883.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22HG3
#5: Protein 50S ribosomal protein L4


Mass: 41992.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7MGP2
#15: Protein 50S ribosomal protein L13


Mass: 45100.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: W7X626
#19: Protein 50S ribosomal protein L17


Mass: 27705.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: A4VE95
#21: Protein 50S ribosomal protein L20


Mass: 20232.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q235I3
#22: Protein 50S ribosomal protein L21


Mass: 27633.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7LVD3
#25: Protein 50S ribosomal protein L24


Mass: 26654.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q24C34
#27: Protein 50S ribosomal protein L27


Mass: 27380.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7M068
#31: Protein 50S ribosomal protein L33


Mass: 7237.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22L35

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Protein , 59 types, 59 molecules AfAgAhAiAjAmAtAzACAFAGAHAKALAMANAOAPAQARASATAUAVBcBdBeBhBjBk...

#6: Protein Ymf69


Mass: 8389.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951A2
#7: Protein Ymf60


Mass: 21681.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951A9
#8: Protein bL7/L12m


Mass: 9039.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
#9: Protein bL7/12m


Mass: 5209.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
#10: Protein bL7/12m


Mass: 5890.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
#13: Protein Ymf74


Mass: 19964.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951B5
#20: Protein bL19m


Mass: 28828.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7M2I9
#26: Protein bL25m


Mass: 37212.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7LVZ3
#29: Protein 39-S ribosomal protein L47


Mass: 36608.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22W36
#32: Protein bL35m


Mass: 19551.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7M803
#33: Protein Ribosomal protein


Mass: 11117.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: W7XH61
#34: Protein mL40


Mass: 23724.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7LT48
#37: Protein mL46


Mass: 36856.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7LWM6
#38: Protein Large subunit ribosomal protein


Mass: 16831.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7MAF1
#39: Protein mL53


Mass: 21995.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22KC0
#40: Protein mL54


Mass: 18240.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7MI39
#41: Protein mL64


Mass: 18191.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q23ZH7
#42: Protein mL101


Mass: 45713.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7M3V9
#43: Protein mL102


Mass: 12872.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: W7WYR3
#44: Protein mL103


Mass: 41557.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7MKV5
#45: Protein mL104


Mass: 90008.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7LTP6
#46: Protein Signal peptide-binding domain protein


Mass: 35486.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: W7XFS0
#47: Protein mL106


Mass: 57790.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q23Q81
#48: Protein Iron-binding zinc finger CDGSH type protein


Mass: 18456.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22HE3
#51: Protein Ymf73


Mass: 19461.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q950X8
#52: Protein Ymf64


Mass: 40101.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951A8
#53: Protein Ymf76


Mass: 50832.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951C0
#56: Protein Ymf63


Mass: 33564.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951A4
#58: Protein Ymf59


Mass: 18389.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q951A1
#59: Protein Ymf61


Mass: 29047.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q950Z8
#68: Protein bS21m


Mass: 12342.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22BA0
#69: Protein mS23


Mass: 63642.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q23YQ0
#70: Protein mS26


Mass: 69412.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7M0P0
#71: Protein Ribosomal death-associated protein


Mass: 83462.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22RT0
#72: Protein mS31


Mass: 83818.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q23UD3
#73: Protein mS33


Mass: 15143.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7LW04
#74: Protein mS34


Mass: 16757.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7LWU8
#75: Protein Ribosomal subunit protein


Mass: 17981.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q23K64
#76: Protein mS37


Mass: 13504.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7MMM6
#78: Protein IGR motif protein


Mass: 15207.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22FZ4
#79: Protein mS45


Mass: 54964.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q23DN6
#81: Protein mS76


Mass: 21735.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q24G80
#82: Protein mS77


Mass: 5379.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
#83: Protein Enoyl-CoA hydratase/isomerase


Mass: 171474.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22P47
#84: Protein mS78


Mass: 179260.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7M7B1
#85: Protein mS79


Mass: 30229.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q23DG3
#86: Protein SelR domain protein


Mass: 36654.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22W57
#87: Protein mS81


Mass: 42317.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q24E31
#88: Protein mS82


Mass: 33603.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22GF7
#89: Protein PARP alpha-helical domain-containing protein,mS83


Mass: 13272.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22N51
#90: Protein mS84,mS84


Mass: 10453.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: PDB-Q22N51
#91: Protein mS85


Mass: 120913.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22UP3
#92: Protein Iron donor protein CyaY


Mass: 16787.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q240K3
#93: Protein mS87


Mass: 127224.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: A4VCP7
#94: Protein mS88


Mass: 25237.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
#95: Protein mS89


Mass: 51871.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22EB6
#96: Protein mS90


Mass: 33264.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q24HL0
#97: Protein mS91


Mass: 24272.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
#99: Protein mS93


Mass: 37252.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7LUK3

-
Protein/peptide , 3 types, 3 molecules ADBCBF

#30: Protein/peptide bL32m


Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
#77: Protein/peptide mS38


Mass: 3166.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
#80: Protein/peptide mS75


Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)

-
30S ribosomal protein ... , 4 types, 4 molecules BfBoBpBq

#54: Protein 30S ribosomal protein S5


Mass: 40865.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7M4M7
#63: Protein 30S ribosomal protein S15


Mass: 23138.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: Q22WF3
#64: Protein 30S ribosomal protein S16


Mass: 52066.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7M3F6
#65: Protein 30S ribosomal protein S17


Mass: 21427.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote)
References: UniProt: I7M6C7

-
Non-polymers , 4 types, 398 molecules

#100: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 393 / Source method: obtained synthetically / Formula: Mg
#101: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#102: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#103: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: The mitochondrial ribosome from tetrahymena thermophila
Type: RIBOSOME / Entity ID: #1-#99 / Source: NATURAL
Molecular weightValue: 4.0 MDa / Experimental value: NO
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)
Buffer solutionpH: 7.45
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 92000 X / Calibrated defocus min: 200 nm / Calibrated defocus max: 3200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 6 sec. / Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 20 / Used frames/image: 2-20

-
Processing

EM software
IDNameVersionCategory
1RELION3.0.7particle selection
4Gctf1.06CTF correction
10RELION3.0.7initial Euler assignment
11RELION3.0.7final Euler assignment
13RELION3.0.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99300 / Symmetry type: POINT

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