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- PDB-7pnu: Assembly intermediate of mouse mitochondrial ribosome small subun... -

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Basic information

Entry
Database: PDB / ID: 7pnu
TitleAssembly intermediate of mouse mitochondrial ribosome small subunit without mS37 in complex with RbfA inward conformation
Components
  • (28S ribosomal protein ...) x 27
  • 12S mitochondrial rRNA
  • Aurora kinase A-interacting protein
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
  • Putative ribosome-binding factor A, mitochondrial
KeywordsRIBOSOME / Assembly intermediate / maturation / biogenesis / small subunit / mitochondrion
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial ribosome binding / anaphase-promoting complex / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / apoptotic mitochondrial changes ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial ribosome binding / anaphase-promoting complex / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / apoptotic mitochondrial changes / positive regulation of proteolysis / ribosomal small subunit binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / regulation of translation / cell junction / nuclear membrane / mitochondrial inner membrane / cell population proliferation / tRNA binding / rRNA binding / protein ubiquitination / ribosome / mitochondrial matrix / structural constituent of ribosome / translation / protein domain specific binding / mRNA binding / intracellular membrane-bounded organelle / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Putative ribosome-binding factor A, mitochondrial / Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 ...Putative ribosome-binding factor A, mitochondrial / Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / 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 / 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 / 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 / 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 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 S10 / 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 / K homology domain-like, alpha/beta / 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 / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9 / Ribosomal protein S11 / Ribosomal protein S17/S11 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S9/S16
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein bS21m / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein mS39 ...ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein bS21m / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein mS39 / Small ribosomal subunit protein mS31 / Putative ribosome-binding factor A, mitochondrial / Small ribosomal subunit protein uS7m / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein mS35 / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS23 / Small ribosomal subunit protein uS2m / Small ribosomal subunit protein mS40 / Small ribosomal subunit protein uS5m / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein uS14m / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein mS33 / Small ribosomal subunit protein uS9m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein mS38 / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein mS34
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsItoh, Y. / Khawaja, A. / Laptev, I. / Sergiev, P. / Rorbach, J. / Amunts, A.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2018-StG-805230European Union
The Swedish Foundation for Strategic ResearchFFL15:0325European Union
European Commission799399-ItohriboEuropean Union
CitationJournal: Nature / Year: 2022
Title: Mechanism of mitoribosomal small subunit biogenesis and preinitiation.
Authors: Yuzuru Itoh / Anas Khawaja / Ivan Laptev / Miriam Cipullo / Ilian Atanassov / Petr Sergiev / Joanna Rorbach / Alexey Amunts /
Abstract: Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) ...Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. ) outcompetes RBFA to complete the assembly with the SSU-mS37-mtIF3 complex that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome.
History
DepositionSep 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 29, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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_initial_refinement_model / pdbx_validate_main_chain_plane / 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.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Jan 17, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 12S mitochondrial rRNA
B: 28S ribosomal protein S2, mitochondrial
C: 28S ribosomal protein S24, mitochondrial
D: 28S ribosomal protein S5, mitochondrial
E: 28S ribosomal protein S6, mitochondrial
F: 28S ribosomal protein S7, mitochondrial
G: 28S ribosomal protein S9, 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
V: 28S ribosomal protein S27, 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
0: 28S ribosomal protein S34, mitochondrial
1: 28S ribosomal protein S35, mitochondrial
3: Aurora kinase A-interacting protein
4: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
a: Putative ribosome-binding factor A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,156,31084
Polymers1,154,09131
Non-polymers2,21953
Water18,3211017
1


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

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 12S mitochondrial rRNA


Mass: 306793.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0

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28S ribosomal protein ... , 27 types, 27 molecules BCDEFGHIJKLMNOPQRSTUVWXYZ01

#2: Protein 28S ribosomal protein S2, mitochondrial / Ribosome / MRP-S2 / S2mt


Mass: 32357.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q924T2
#3: Protein 28S ribosomal protein S24, mitochondrial / Ribosome / MRP-S24 / S24mt


Mass: 18934.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9CQV5
#4: Protein 28S ribosomal protein S5, mitochondrial / Ribosome / MRP-S5 / S5mt


Mass: 48293.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q99N87
#5: Protein 28S ribosomal protein S6, mitochondrial / Ribosome / MRP-S6 / S6mt


Mass: 14333.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: P58064
#6: Protein 28S ribosomal protein S7, mitochondrial / Ribosome / MRP-S7 / S7mt


Mass: 28112.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q80X85
#7: Protein 28S ribosomal protein S9, mitochondrial / Ribosome / MRP-S9 / S9mt


Mass: 44997.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9D7N3
#8: Protein 28S ribosomal protein S10, mitochondrial / Ribosome / MRP-S10 / S10mt


Mass: 18729.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q80ZK0
#9: Protein 28S ribosomal protein S11, mitochondrial / Ribosome / MRP-S11 / S11mt


Mass: 20252.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9DCA2
#10: Protein 28S ribosomal protein S12, mitochondrial / Ribosome / MRP-S12 / S12mt / MT-RPS12


Mass: 15469.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: O35680
#11: Protein 28S ribosomal protein S14, mitochondrial / Ribosome / MRP-S14 / S14mt


Mass: 14949.552 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9CR88
#12: Protein 28S ribosomal protein S15, mitochondrial / Ribosome / MRP-S15 / S15mt


Mass: 29523.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9DC71
#13: Protein 28S ribosomal protein S16, mitochondrial / Ribosome / MRP-S16 / S16mt


Mass: 15218.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9CPX7
#14: Protein 28S ribosomal protein S17, mitochondrial / Ribosome / MRP-S17 / S17mt


Mass: 13405.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9CQE3
#15: Protein 28S ribosomal protein S18b, mitochondrial / Ribosome / MRP-S18-b / Mrps18-b / S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2


Mass: 28740.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q99N84
#16: Protein 28S ribosomal protein S18c, mitochondrial / Ribosome / MRP-S18-c / Mrps18-c / S18mt-c / 28S ribosomal protein S18-1 / mitochondrial / MRP-S18-1


Mass: 16300.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q8R2L5
#17: Protein 28S ribosomal protein S21, mitochondrial / Ribosome / MRP-S21 / S21mt


Mass: 10493.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: P58059
#18: Protein 28S ribosomal protein S22, mitochondrial / Ribosome / MRP-S22 / S22mt


Mass: 41255.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9CXW2
#19: Protein 28S ribosomal protein S23, mitochondrial / Ribosome / MRP-S23 / S23mt


Mass: 20378.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q8VE22
#20: Protein 28S ribosomal protein S25, mitochondrial / Ribosome / MRP-S25 / S25mt


Mass: 19950.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9D125
#21: Protein 28S ribosomal protein S26, mitochondrial / Ribosome / MRP-S26 / S26mt


Mass: 23484.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q80ZS3
#22: Protein 28S ribosomal protein S27, mitochondrial / Ribosome / MRP-S27 / S27mt / Mitochondrial ribosomal protein S27


Mass: 47836.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q8BK72
#23: Protein 28S ribosomal protein S28, mitochondrial / Ribosome / MRP-S28 / S28mt


Mass: 20555.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9CY16
#24: Protein 28S ribosomal protein S29, mitochondrial / Ribosome / MRP-S29 / S29mt / Death-associated protein 3 / DAP-3


Mass: 44766.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9ER88
#25: Protein 28S ribosomal protein S31, mitochondrial / Ribosome / MRP-S31 / S31mt / Imogen 38


Mass: 43950.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q61733
#26: Protein 28S ribosomal protein S33, mitochondrial / Ribosome / MRP-S33 / S33mt / Ganglioside-induced differentiation-associated-protein 3


Mass: 12487.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9D2R8
#27: Protein 28S ribosomal protein S34, mitochondrial / Ribosome / MRP-S34 / S34mt / T-complex expressed gene 2 protein


Mass: 25874.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9JIK9
#28: Protein 28S ribosomal protein S35, mitochondrial / Ribosome / MRP-S35 / S35mt


Mass: 36028.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q8BJZ4

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Protein , 3 types, 3 molecules 34a

#29: Protein Aurora kinase A-interacting protein / AURKA-interacting protein / 28S ribosomal protein S38 / mitochondrial / MRP-S38


Mass: 23345.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9DCJ7
#30: Protein Pentatricopeptide repeat domain-containing protein 3, mitochondrial / 28S ribosomal protein S39 / mitochondrial / MRP-S39


Mass: 77890.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q14C51
#31: Protein Putative ribosome-binding factor A, mitochondrial


Mass: 39382.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q6P3B9

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Non-polymers , 6 types, 1070 molecules

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


Mass: 24.305 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: Mg
#33: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#34: Chemical ChemComp-ZN / ZINC ION


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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#36: 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
#37: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1017 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: Assembly intermediate of small subunit of human mitochondrial ribosome
Type: RIBOSOME / Entity ID: #1-#31 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
10.20 Mpotassium chlorideKCl1
25.0 mMmagnesium acetateMg(CH3COO)21
325 mMHEPES-KOH buffer pH 7.51
40.05 % (w/v)n-dodecyl-beta-D-maltopyranosideC24H46O111
50.25 mM5'-guanylyl imidodiphosphateC10H17N6O13P31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 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: 165000 X / Nominal defocus max: 3600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 31 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 26468
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20 / Used frames/image: 1-20

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7Coot0.8model fitting
9PHENIX1.18model refinement
10RELION3initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3076615
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26468 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 6RW4

6rw4


Accession code: 6RW4 / Source name: PDB / Type: experimental model

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