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- PDB-8ois: 28S human mitochondrial small ribosomal subunit with mtRF1 and P-... -

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Entry
Database: PDB / ID: 8ois
Title28S human mitochondrial small ribosomal subunit with mtRF1 and P-site tRNA
Components
  • (28S ribosomal protein ...) x 27
  • (39S ribosomal protein ...) x 2
  • 12S rRNAMT-RNR1
  • Aurora kinase A-interacting protein
  • Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
  • P-site Met-tRNA(Met)
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
  • Peptide chain release factor 1, mitochondrial,mtRF1(AAQ)
  • mRNAMessenger RNA
KeywordsRIBOSOME / human mitochondrial ribosome / release factor mtRF1 / non-canonical stop codon
Function / homology
Function and homology information


mitochondrial ribosome binding / translation release factor activity / mitochondrial translational termination / mitochondrial ribosome assembly / translation release factor activity, codon specific / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / negative regulation of mitotic nuclear division ...mitochondrial ribosome binding / translation release factor activity / mitochondrial translational termination / mitochondrial ribosome assembly / translation release factor activity, codon specific / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / apoptotic signaling pathway / small ribosomal subunit rRNA binding / fibrillar center / ribosomal small subunit assembly / regulation of translation / cell junction / small ribosomal subunit / nuclear membrane / mitochondrial inner membrane / cell population proliferation / tRNA binding / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / translation / protein domain specific binding / mRNA binding / intracellular membrane-bounded organelle / synapse / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Peptide chain release factor / 28S ribosomal protein S26 / PCRF domain / Mitochondrial ribosome subunit S26 / PCRF / PPR repeat family / Cysteine alpha-hairpin motif superfamily / Peptide chain release factor class I superfamily / 28S ribosomal protein S27, mitochondrial ...Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Peptide chain release factor / 28S ribosomal protein S26 / PCRF domain / Mitochondrial ribosome subunit S26 / PCRF / PPR repeat family / Cysteine alpha-hairpin motif superfamily / Peptide chain release factor class I superfamily / 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 / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / 28S ribosomal protein S24, mitochondrial / Mitochondrial 28S ribosomal protein S34 / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / Mitochondrial ribosome subunit S24 / Mitochondrial 28S ribosomal protein S34 / 40S ribosomal protein rpS2 (S5p), N-terminal / Prokaryotic-type class I peptide chain release factors signature. / 28S ribosomal protein S25, mitochondrial / Pentatricopeptide repeat domain / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / Mitochondrial ribosomal protein L55 / 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) / Peptide chain release factor class I / RF-1 domain / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / 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 / Ribosomal protein S16 domain superfamily / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / 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 S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S14 / Ribosomal protein S2 / Ribosomal protein S14p/S29e / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal S11, conserved site / Ribosomal protein S10p/S20e / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S5, N-terminal domain / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S5, C-terminal domain / Ribosomal protein S11
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FE-S-O HYBRID CLUSTER / GUANOSINE-5'-DIPHOSPHATE / : / METHIONINE / : / : / RNA / RNA (> 10) / RNA (> 100) ...ADENOSINE-5'-TRIPHOSPHATE / FE-S-O HYBRID CLUSTER / GUANOSINE-5'-DIPHOSPHATE / : / METHIONINE / : / : / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS14m / Peptide chain release factor 1, mitochondrial / Large ribosomal subunit protein bL19m / 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 / Large ribosomal subunit protein mL55 / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS31 / Small ribosomal subunit protein mS37 / 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: 3 Å
AuthorsSaurer, M. / Leibundgut, M. / Scaiola, A. / Schoenhut, T. / Ban, N.
Funding support Switzerland, European Union, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation182341 Switzerland
Swiss National Science Foundation179190 Switzerland
European Molecular Biology Organization (EMBO)1074-2019European Union
CitationJournal: Science / Year: 2023
Title: Molecular basis of translation termination at noncanonical stop codons in human mitochondria.
Authors: Martin Saurer / Marc Leibundgut / Hima Priyanka Nadimpalli / Alain Scaiola / Tanja Schönhut / Richard G Lee / Stefan J Siira / Oliver Rackham / René Dreos / Tea Lenarčič / Eva Kummer / ...Authors: Martin Saurer / Marc Leibundgut / Hima Priyanka Nadimpalli / Alain Scaiola / Tanja Schönhut / Richard G Lee / Stefan J Siira / Oliver Rackham / René Dreos / Tea Lenarčič / Eva Kummer / David Gatfield / Aleksandra Filipovska / Nenad Ban /
Abstract: The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the ...The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons.
History
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _em_3d_fitting_list.initial_refinement_model_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Apr 24, 2024Group: Data collection / Structure summary / Category: chem_comp / chem_comp_atom / chem_comp_bond
Item: _chem_comp.pdbx_synonyms / _chem_comp_atom.atom_id ..._chem_comp.pdbx_synonyms / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
BX: 39S ribosomal protein L19, mitochondrial
Bd: 39S ribosomal protein L55, mitochondrial
AA: 12S rRNA
AB: 28S ribosomal protein S35, mitochondrial
AC: 28S ribosomal protein S24, mitochondrial
AD: Aurora kinase A-interacting protein
AE: 28S ribosomal protein S6, mitochondrial
AF: 28S ribosomal protein S7, mitochondrial
AG: P-site Met-tRNA(Met)
AH: 28S ribosomal protein S10, mitochondrial
AI: mRNA
AJ: 28S ribosomal protein S12, mitochondrial
AK: 28S ribosomal protein S14, mitochondrial
AL: 28S ribosomal protein S15, mitochondrial
AM: 28S ribosomal protein S16, mitochondrial
AN: 28S ribosomal protein S17, mitochondrial
AO: 28S ribosomal protein S18b, mitochondrial
AP: 28S ribosomal protein S18c, mitochondrial
AQ: 28S ribosomal protein S21, mitochondrial
AR: 28S ribosomal protein S22, mitochondrial
AS: 28S ribosomal protein S23, mitochondrial
AT: 28S ribosomal protein S25, mitochondrial
AU: 28S ribosomal protein S26, mitochondrial
AV: 28S ribosomal protein S27, mitochondrial
AW: 28S ribosomal protein S28, mitochondrial
AX: 28S ribosomal protein S29, mitochondrial
AY: 28S ribosomal protein S31, mitochondrial
AZ: 28S ribosomal protein S33, mitochondrial
Aa: Peptide chain release factor 1, mitochondrial,mtRF1(AAQ)
Ab: 28S ribosomal protein S2, mitochondrial
Ac: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
Ad: 28S ribosomal protein S5, mitochondrial
Ae: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
Ag: 28S ribosomal protein S9, mitochondrial
Ai: 28S ribosomal protein S11, mitochondrial
Aj: 28S ribosomal protein S34, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,282,874185
Polymers1,277,31136
Non-polymers5,563149
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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39S ribosomal protein ... , 2 types, 2 molecules BXBd

#1: Protein 39S ribosomal protein L19, mitochondrial / Ribosome / MRP-L19 / 39S ribosomal protein L15 / mitochondrial / MRP-L15 / Mitochondrial large ribosomal ...MRP-L19 / 39S ribosomal protein L15 / mitochondrial / MRP-L15 / Mitochondrial large ribosomal subunit protein bL19m


Mass: 33584.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P49406
#2: Protein 39S ribosomal protein L55, mitochondrial / Ribosome / MRP-L55 / Mitochondrial large ribosomal subunit protein bL31m / Mitochondrial large ribosomal ...MRP-L55 / Mitochondrial large ribosomal subunit protein bL31m / Mitochondrial large ribosomal subunit protein mL55


Mass: 15160.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q7Z7F7

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RNA chain , 3 types, 3 molecules AAAGAI

#3: RNA chain 12S rRNA / MT-RNR1


Mass: 306547.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: NCBI Reference Sequence: NC_012920.1 + one C at 3'-end (encoded but not annotated as part of the sequence), a A103>G and A791>G as found in e.g. GenBank: OM714795.1
Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: GenBank: OM714795.1
#9: RNA chain P-site Met-tRNA(Met)


Mass: 22692.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: NCBI Reference Sequence: NC_012920.1 + aminoacylated CCA-end
Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: GenBank: NC_012920.1
#11: RNA chain mRNA / Messenger RNA


Mass: 7329.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence as observed in the cryo-EM density map. / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA

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28S ribosomal protein ... , 27 types, 27 molecules ABACAEAFAHAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAbAdAgAiAj

#4: Protein 28S ribosomal protein S35, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: P82673
#5: Protein 28S ribosomal protein S24, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q96EL2
#7: Protein 28S ribosomal protein S6, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: P82932
#8: Protein 28S ribosomal protein S7, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q9Y2R9
#10: Protein 28S ribosomal protein S10, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: P82664
#12: Protein 28S ribosomal protein S12, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: O15235
#13: Protein 28S ribosomal protein S14, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: O60783
#14: Protein 28S ribosomal protein S15, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: P82914
#15: Protein 28S ribosomal protein S16, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q9Y3D3
#16: Protein 28S ribosomal protein S17, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q9Y2R5
#17: Protein 28S ribosomal protein S18b, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q9Y676
#18: Protein 28S ribosomal protein S18c, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q9Y3D5
#19: Protein 28S ribosomal protein S21, mitochondrial / Ribosome / MRP-S21 / S21mt / Mitochondrial small ribosomal subunit protein bS21m


Mass: 10806.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GenBank: AAH04566.2 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82921
#20: Protein 28S ribosomal protein S22, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: P82650
#21: Protein 28S ribosomal protein S23, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q9Y3D9
#22: Protein 28S ribosomal protein S25, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: P82663
#23: Protein 28S ribosomal protein S26, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q9BYN8
#24: Protein 28S ribosomal protein S27, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q92552
#25: Protein 28S ribosomal protein S28, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q9Y2Q9
#26: Protein 28S ribosomal protein S29, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: P51398
#27: Protein 28S ribosomal protein S31, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q92665
#28: Protein 28S ribosomal protein S33, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q9Y291
#30: Protein 28S ribosomal protein S2, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: Q9Y399
#32: Protein 28S ribosomal protein S5, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: P82675
#34: Protein 28S ribosomal protein S9, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: P82933
#35: Protein 28S ribosomal protein S11, mitochondrial / Ribosome / MRP-S11 / S11mt / Cervical cancer proto-oncogene 2 protein / HCC-2 / Mitochondrial small ribosomal ...MRP-S11 / S11mt / Cervical cancer proto-oncogene 2 protein / HCC-2 / Mitochondrial small ribosomal subunit protein uS11m


Mass: 20663.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: P82912
#36: Protein 28S ribosomal protein S34, mitochondrial / Ribosome / 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) / Cell line: HEK293 EBNA / References: UniProt: P82930

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Protein , 4 types, 4 molecules ADAaAcAe

#6: 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) / Cell line: HEK293 EBNA / References: UniProt: Q9NWT8
#29: Protein Peptide chain release factor 1, mitochondrial,mtRF1(AAQ) / MRF-1 / MtRF-1


Mass: 56258.391 Da / Num. of mol.: 1 / Mutation: 311GGQ313 > AAQ / Source method: isolated from a natural source
Details: Human mitochondrial release factor 1 (mtRF1), containing a 311GGQ>AAQ mutation, a C-terminal linker (GGSGGSGGSGGSGGSGG) and a 3xFLAG-tag (DYKDHDGDYKDHDIDYKDDDDK), expressed from a pcDNA3.1(+) ...Details: Human mitochondrial release factor 1 (mtRF1), containing a 311GGQ>AAQ mutation, a C-terminal linker (GGSGGSGGSGGSGGSGG) and a 3xFLAG-tag (DYKDHDGDYKDHDIDYKDDDDK), expressed from a pcDNA3.1(+) plasmid in HEK293 EBNA cells.,Human mitochondrial release factor 1 (mtRF1), containing a 311GGQ>AAQ mutation, a C-terminal linker (GGSGGSGGSGGSGGSGG) and a 3xFLAG-tag (DYKDHDGDYKDHDIDYKDDDDK), expressed from a pcDNA3.1(+) plasmid in HEK293 EBNA cells.
Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: O75570
#31: Protein Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S37 / mitochondrial / MRP-S37 / Mitochondrial small ribosomal subunit protein ...28S ribosomal protein S37 / mitochondrial / MRP-S37 / Mitochondrial small ribosomal subunit protein mS37 / Nuclear protein C2360


Mass: 13540.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 EBNA / References: UniProt: Q96BP2
#33: 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) / Cell line: HEK293 EBNA / References: UniProt: Q96EY7

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Non-polymers , 8 types, 152 molecules

#37: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: K
#38: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 126 / Source method: obtained synthetically / Formula: Mg
#39: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#40: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#41: Chemical ChemComp-FS2 / FE-S-O HYBRID CLUSTER


Mass: 335.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4O3S2
#42: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#43: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#44: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 28S human mitochondrial small ribosomal subunit with mtRF1, mRNA, and P-site tRNA
Type: RIBOSOME
Details: 28S human mitochondrial small ribosomal subunit in complex with mtRF1(AAQ)-3xFLAG, human methionine-tRNA(Met), and an mRNA containing a non-canonical stop codon, purified from HEK293 EBNA cells.
Entity ID: #1-#36 / Source: NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.1 MDaNO
211.1 MDaNO
310.03 MDaNO
410.05 MDaYES
510.05 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDCellular locationOrganelle
21Homo sapiens (human)9606Mitochondrial matrixMitochondrion
41Homo sapiens (human)9606Mitochondrial matrixMitochondrion
51Homo sapiens (human)9606Mitochondrial matrixMitochondria
61Homo sapiens (human)9606Mitochondrial matrixMitochondrion
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCellPlasmid
41Homo sapiens (human)9606HEK293 EBNApcDNA3.1(+)
51Homo sapiens (human)9606HEK293 EBNAHEK293 EBNApcDNA3.1(+)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMpotassium chlorideKCl1
320 mMmagnesium chlorideMgCl21
41 mMDTTHSCH2CH(OH)CH(OH)CH2SH1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Affinity-purified 55S mitoribosome. Refinement focused on 28S small subunit.
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 43882
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2EPUimage acquisition
4cryoSPARC4CTF correction
7Coot0.9.8.4model fitting
9cryoSPARC4initial Euler assignment
10cryoSPARC4final Euler assignment
12cryoSPARC43D reconstruction
13PHENIX1.20.1model refinement
Image processingDetails: Micrographs were motion corrected and CTF parameters were estimated using Cryosparc.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5423665
Details: Particles were picked with blob picker in Cryosparc.
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41288 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeDetailsInitial refinement model-IDSource nameType
17QI4

7qi4

7QI4High-res mammalian mitoribosome1PDBexperimental model
2UniProt AF-O75570-F1human mtRF1 model prediction2AlphaFoldin silico model

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