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- PDB-8qrk: mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 1 -

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Basic information

Entry
Database: PDB / ID: 8qrk
Titlemt-SSU assembly intermediate in GTPBP8 knock-out cells, state 1
Components
  • (28S ribosomal protein ...) x 27
  • 12S mitochondrial rRNA
  • Aurora kinase A-interacting protein
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
KeywordsRIBOSOME / Mitochondria / Assembly / GTPBP8
Function / homology
Function and homology information


mitochondrial ribosome binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / negative regulation of mitotic nuclear division / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation ...mitochondrial ribosome binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / positive regulation of mitochondrial translation / negative regulation of mitotic nuclear division / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / Mitochondrial protein degradation / apoptotic signaling pathway / small ribosomal subunit rRNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / nuclear membrane / cell population proliferation / tRNA binding / mitochondrial inner membrane / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleolus / GTP binding / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Ribosomal protein S22, mitochondrial / Ribosomal protein S23, mitochondrial / Ribosomal protein S23/S25, mitochondrial / Mitochondrial 28S ribosomal protein S31 / : ...28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Ribosomal protein S22, mitochondrial / Ribosomal protein S23, mitochondrial / Ribosomal protein S23/S25, mitochondrial / Mitochondrial 28S ribosomal protein S31 / : / Mitochondrial 28S ribosomal protein S22 / Mitochondrial ribosomal protein S23 / Mitochondrial 28S ribosomal protein S31 / Ribosomal protein S29, mitochondrial / Ribosomal protein S28, mitochondrial / Mitochondrial 28S ribosomal protein S34 / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / Mitochondrial 28S ribosomal protein S34 / 28S ribosomal protein S24, mitochondrial / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / Mitochondrial ribosome subunit S24 / Small ribosomal subunit protein uS5m, N-terminal / Small ribosomal subunit protein mS39, PPR / 28S ribosomal protein S25, mitochondrial / Pentatricopeptide repeat domain / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Pentatricopeptide (PPR) repeat profile. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S11 / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S11 / Ribosomal protein S12 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / STREPTOMYCIN / : / RNA / RNA (> 10) ...ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / STREPTOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS14m / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein mS35 / Small ribosomal subunit protein uS5m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein bS21m / Small ribosomal subunit protein mS34 / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein uS9m / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS31 / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS39 / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein mS38 / Small ribosomal subunit protein mS33 / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein uS7m / Small ribosomal subunit protein uS2m / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS23 / Small ribosomal subunit protein mS40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.69 Å
AuthorsValentin Gese, G. / Cipullo, M. / Rorbach, J. / Hallberg, B.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: GTPBP8 plays a role in mitoribosome formation in human mitochondria.
Authors: Miriam Cipullo / Genís Valentín Gesé / Shreekara Gopalakrishna / Annika Krueger / Vivian Lobo / Maria A Pirozhkova / James Marks / Petra Páleníková / Dmitrii Shiriaev / Yong Liu / ...Authors: Miriam Cipullo / Genís Valentín Gesé / Shreekara Gopalakrishna / Annika Krueger / Vivian Lobo / Maria A Pirozhkova / James Marks / Petra Páleníková / Dmitrii Shiriaev / Yong Liu / Jelena Misic / Yu Cai / Minh Duc Nguyen / Abubakar Abdelbagi / Xinping Li / Michal Minczuk / Markus Hafner / Daniel Benhalevy / Aishe A Sarshad / Ilian Atanassov / B Martin Hällberg / Joanna Rorbach /
Abstract: Mitochondrial gene expression relies on mitoribosomes to translate mitochondrial mRNAs. The biogenesis of mitoribosomes is an intricate process involving multiple assembly factors. Among these ...Mitochondrial gene expression relies on mitoribosomes to translate mitochondrial mRNAs. The biogenesis of mitoribosomes is an intricate process involving multiple assembly factors. Among these factors, GTP-binding proteins (GTPBPs) play important roles. In bacterial systems, numerous GTPBPs are required for ribosome subunit maturation, with EngB being a GTPBP involved in the ribosomal large subunit assembly. In this study, we focus on exploring the function of GTPBP8, the human homolog of EngB. We find that ablation of GTPBP8 leads to the inhibition of mitochondrial translation, resulting in significant impairment of oxidative phosphorylation. Structural analysis of mitoribosomes from GTPBP8 knock-out cells shows the accumulation of mitoribosomal large subunit assembly intermediates that are incapable of forming functional monosomes. Furthermore, fPAR-CLIP analysis reveals that GTPBP8 is an RNA-binding protein that interacts specifically with the mitochondrial ribosome large subunit 16 S rRNA. Our study highlights the role of GTPBP8 as a component of the mitochondrial gene expression machinery involved in mitochondrial large subunit maturation.
History
DepositionOct 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 28S ribosomal protein S34, mitochondrial
1: 28S ribosomal protein S35, mitochondrial
3: Aurora kinase A-interacting protein
A: 12S mitochondrial rRNA
B: 28S ribosomal protein S2, mitochondrial
C: 28S ribosomal protein S24, mitochondrial
E: 28S ribosomal protein S6, mitochondrial
F: 28S ribosomal protein S7, mitochondrial
H: 28S ribosomal protein S10, mitochondrial
I: 28S ribosomal protein S11, mitochondrial
J: 28S ribosomal protein S12, mitochondrial
K: 28S ribosomal protein S14, mitochondrial
L: 28S ribosomal protein S15, mitochondrial
M: 28S ribosomal protein S16, mitochondrial
N: 28S ribosomal protein S17, mitochondrial
O: 28S ribosomal protein S18b, mitochondrial
P: 28S ribosomal protein S18c, mitochondrial
Q: 28S ribosomal protein S21, mitochondrial
R: 28S ribosomal protein S22, mitochondrial
S: 28S ribosomal protein S23, mitochondrial
T: 28S ribosomal protein S25, mitochondrial
U: 28S ribosomal protein S26, mitochondrial
W: 28S ribosomal protein S28, mitochondrial
X: 28S ribosomal protein S29, mitochondrial
Y: 28S ribosomal protein S31, mitochondrial
Z: 28S ribosomal protein S33, mitochondrial
D: 28S ribosomal protein S5, mitochondrial
G: 28S ribosomal protein S9, mitochondrial
V: 28S ribosomal protein S27, mitochondrial
4: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,133,347104
Polymers1,128,59830
Non-polymers4,74974
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area202660 Å2
ΔGint-1743 kcal/mol
Surface area366130 Å2

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Components

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28S ribosomal protein ... , 27 types, 27 molecules 01BCEFHIJKLMNOPQRSTUWXYZDGV

#1: Protein 28S ribosomal protein S34, mitochondrial / S34mt / Mitochondrial small ribosomal subunit protein mS34


Mass: 25695.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82930
#2: Protein 28S ribosomal protein S35, mitochondrial / MRP-S35 / S35mt / 28S ribosomal protein S28 / mitochondrial / MRP-S28 / S28mt / Mitochondrial small ...MRP-S35 / S35mt / 28S ribosomal protein S28 / mitochondrial / MRP-S28 / S28mt / Mitochondrial small ribosomal subunit protein mS35


Mass: 36898.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82673
#5: Protein 28S ribosomal protein S2, mitochondrial / MRP-S2 / S2mt / Mitochondrial small ribosomal subunit protein uS2m


Mass: 33298.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y399
#6: Protein 28S ribosomal protein S24, mitochondrial / MRP-S24 / S24mt / Mitochondrial small ribosomal subunit protein uS3m / bMRP-47 / bMRP47


Mass: 19046.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EL2
#7: Protein 28S ribosomal protein S6, mitochondrial / MRP-S6 / S6mt / Mitochondrial small ribosomal subunit protein bS6m


Mass: 14250.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82932
#8: Protein 28S ribosomal protein S7, mitochondrial / MRP-S7 / S7mt / Mitochondrial small ribosomal subunit protein uS7m / bMRP-27a / bMRP27a


Mass: 28186.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2R9
#9: Protein 28S ribosomal protein S10, mitochondrial / MRP-S10 / S10mt / Mitochondrial small ribosomal subunit protein uS10m


Mass: 23033.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82664
#10: Protein 28S ribosomal protein S11, mitochondrial / S11mt / Cervical cancer proto-oncogene 2 protein / HCC-2 / Mitochondrial small ribosomal subunit protein uS11m


Mass: 20648.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82912
#11: Protein 28S ribosomal protein S12, mitochondrial / MRP-S12 / S12mt / MT-RPS12 / Mitochondrial small ribosomal subunit protein uS12m


Mass: 15200.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15235
#12: Protein 28S ribosomal protein S14, mitochondrial / MRP-S14 / S14mt / Mitochondrial small ribosomal subunit protein uS14m


Mass: 15168.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60783
#13: Protein 28S ribosomal protein S15, mitochondrial / MRP-S15 / S15mt / Mitochondrial small ribosomal subunit protein uS15m


Mass: 29903.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82914
#14: Protein 28S ribosomal protein S16, mitochondrial / MRP-S16 / S16mt / Mitochondrial small ribosomal subunit protein bS16m


Mass: 15371.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3D3
#15: Protein 28S ribosomal protein S17, mitochondrial / MRP-S17 / S17mt / Mitochondrial small ribosomal subunit protein uS17m


Mass: 14526.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2R5
#16: Protein 28S ribosomal protein S18b, mitochondrial / MRP-S18-b / Mrps18-b / S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2 / ...MRP-S18-b / Mrps18-b / S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2 / Mitochondrial small ribosomal subunit protein bS18b / Mitochondrial small ribosomal subunit protein mS40


Mass: 29440.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y676
#17: Protein 28S ribosomal protein S18c, mitochondrial / MRP-S18-c / Mrps18-c / S18mt-c / 28S ribosomal protein S18-1 / mitochondrial / MRP-S18-1 / ...MRP-S18-c / Mrps18-c / S18mt-c / 28S ribosomal protein S18-1 / mitochondrial / MRP-S18-1 / Mitochondrial small ribosomal subunit protein bS18c / Mitochondrial small ribosomal subunit protein bS18m


Mass: 15876.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3D5
#18: Protein 28S ribosomal protein S21, mitochondrial / S21mt / Mitochondrial small ribosomal subunit protein bS21m


Mass: 10675.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82921
#19: Protein 28S ribosomal protein S22, mitochondrial / MRP-S22 / S22mt / Mitochondrial small ribosomal subunit protein mS22


Mass: 41337.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82650
#20: Protein 28S ribosomal protein S23, mitochondrial / MRP-S23 / S23mt / Mitochondrial small ribosomal subunit protein mS23


Mass: 21805.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3D9
#21: Protein 28S ribosomal protein S25, mitochondrial / MRP-S25 / S25mt / Mitochondrial small ribosomal subunit protein mS25


Mass: 20146.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82663
#22: Protein 28S ribosomal protein S26, mitochondrial / MRP-S26 / S26mt / 28S ribosomal protein S13 / mitochondrial / MRP-S13 / S13mt / Mitochondrial small ...MRP-S26 / S26mt / 28S ribosomal protein S13 / mitochondrial / MRP-S13 / S13mt / Mitochondrial small ribosomal subunit protein mS26


Mass: 24259.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYN8
#23: Protein 28S ribosomal protein S28, mitochondrial / MRP-S28 / S28mt / 28S ribosomal protein S35 / mitochondrial / MRP-S35 / S35mt / Mitochondrial small ...MRP-S28 / S28mt / 28S ribosomal protein S35 / mitochondrial / MRP-S35 / S35mt / Mitochondrial small ribosomal subunit protein bS1m


Mass: 20878.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2Q9
#24: Protein 28S ribosomal protein S29, mitochondrial / MRP-S29 / S29mt / Death-associated protein 3 / DAP-3 / Ionizing radiation resistance conferring ...MRP-S29 / S29mt / Death-associated protein 3 / DAP-3 / Ionizing radiation resistance conferring protein / Mitochondrial small ribosomal subunit protein mS29


Mass: 45634.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51398
#25: Protein 28S ribosomal protein S31, mitochondrial / MRP-S31 / S31mt / Imogen 38 / Mitochondrial small ribosomal subunit protein mS31


Mass: 45391.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92665
#26: Protein 28S ribosomal protein S33, mitochondrial / MRP-S33 / S33mt / Mitochondrial small ribosomal subunit protein mS33


Mass: 12657.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y291
#27: Protein 28S ribosomal protein S5, mitochondrial / MRP-S5 / S5mt / Mitochondrial small ribosomal subunit protein uS5m


Mass: 48094.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82675
#28: Protein 28S ribosomal protein S9, mitochondrial / MRP-S9 / S9mt / Mitochondrial small ribosomal subunit protein uS9m


Mass: 45909.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82933
#29: Protein 28S ribosomal protein S27, mitochondrial / MRP-S27 / S27mt / Mitochondrial ribosomal protein S27 / Mitochondrial small ribosomal subunit protein mS27


Mass: 47669.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92552

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Protein , 2 types, 2 molecules 34

#3: Protein Aurora kinase A-interacting protein / AURKA-interacting protein / 28S ribosomal protein S38 / mitochondrial / MRP-S38 / Mitochondrial ...AURKA-interacting protein / 28S ribosomal protein S38 / mitochondrial / MRP-S38 / Mitochondrial small ribosomal subunit protein mS38


Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWT8
#30: Protein Pentatricopeptide repeat domain-containing protein 3, mitochondrial / 28S ribosomal protein S39 / mitochondrial / MRP-S39 / Mitochondrial small ribosomal subunit protein ...28S ribosomal protein S39 / mitochondrial / MRP-S39 / Mitochondrial small ribosomal subunit protein mS39 / Transformation-related gene 15 protein / TRG-15


Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY7

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RNA chain , 1 types, 1 molecules A

#4: RNA chain 12S mitochondrial rRNA


Mass: 306547.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: OM714795.1

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Non-polymers , 9 types, 74 molecules

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


Mass: 24.305 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: Mg
#32: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#33: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#34: Chemical ChemComp-SRY / STREPTOMYCIN / STREPTOMYCIN A


Mass: 581.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H39N7O12 / Comment: medication, antibiotic*YM
#35: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: K
#36: Chemical ChemComp-ZN / ZINC ION


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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#38: 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
#39: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: mtSSU assembly intermediate (State 1) / Type: CELL
Entity ID: #1-#3, #30, #4-#6, #27, #7-#8, #28, #9-#22, #29, #23-#26
Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: Ice
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1Warpparticle selection
4WarpCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 435172
3D reconstructionResolution: 6.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53380 / Symmetry type: POINT

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