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- PDB-9hcd: Mouse mitoribosome large subunit assembly intermediate (with uL16... -

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Basic information

Entry
Database: PDB / ID: 9hcd
TitleMouse mitoribosome large subunit assembly intermediate (with uL16m) bound to MRM3-dimer, DDX28 and the MALSU-L0R8F8-mt-ACP complex, state A2 (SAMC knock-out)
Components
  • (Large ribosomal subunit protein ...) x 44
  • 16S rRNA (1584-MER)
  • Acyl carrier protein, mitochondrial
  • Mitochondrial assembly of ribosomal large subunit protein 1
  • Predicted gene, 55359
  • Probable ATP-dependent RNA helicase DDX28
  • rRNA methyltransferase 3, mitochondrial
  • tRNA-Phe (68-MER)
KeywordsRIBOSOME / mitochondria / large subunit / assembly intermediate
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / rRNA (guanosine-2'-O-)-methyltransferase activity / ribonucleoprotein granule / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / positive regulation of mitochondrial translation ...Mitochondrial translation elongation / Mitochondrial translation termination / rRNA (guanosine-2'-O-)-methyltransferase activity / ribonucleoprotein granule / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / positive regulation of mitochondrial translation / Respiratory electron transport / rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial translational elongation / ribonuclease III activity / : / translation release factor activity, codon nonspecific / Mitochondrial protein degradation / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit / mitochondrial fission / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit binding / peptidyl-tRNA hydrolase / mitochondrial ribosome / mitochondrial small ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase activity / mitochondrial translation / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / mitochondrial respiratory chain complex I assembly / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / respiratory chain complex I / RNA processing / cytosolic ribosome / rescue of stalled ribosome / aerobic respiration / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to leukemia inhibitory factor / ribosomal large subunit biogenesis / fatty acid biosynthetic process / cell junction / double-stranded RNA binding / 5S rRNA binding / RNA helicase activity / mitochondrial inner membrane / rRNA binding / nuclear body / structural constituent of ribosome / RNA helicase / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / apoptotic process / nucleolus / structural molecule activity / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
RNA 2-O ribose methyltransferase, substrate binding / : / MRM3-like substrate binding domain / RNA 2'-O ribose methyltransferase substrate binding / : / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / MIEF1-MP, LYR domain / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation ...RNA 2-O ribose methyltransferase, substrate binding / : / MRM3-like substrate binding domain / RNA 2'-O ribose methyltransferase substrate binding / : / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / MIEF1-MP, LYR domain / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / : / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Ribosomal protein S30, mitochondrial / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein L37, mitochondrial / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal protein L28 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L51, mitochondrial / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Ribosomal protein L37/S30 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / : / : / Mitochondrial 28S ribosomal protein S30 (PDCD9) / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / : / MRPL44, double-stranded RNA binding domain / : / MRPL44 dsRNA-binding domain / Large ribosomal subunit protein mL44, endonuclease domain / : / : / Large ribosomal subunit protein bL9m C-terminal domain / Large ribosomal subunit protein bL9m N-terminal domain / Tim44-like domain / Tim44-like domain / Tim44 / : / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal subunit 39S / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / : / Mitochondrial ribosomal protein L27 / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS-like / TGS domain profile. / TGS / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / : / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Beta-grasp domain superfamily / NTF2-like domain superfamily / Acyl carrier protein (ACP) / NUDIX hydrolase-like domain superfamily / Ribosomal protein L11, bacterial-type / Nucleotidyltransferase superfamily / Phosphopantetheine attachment site / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Phosphopantetheine attachment site. / Ribosomal protein L10-like domain superfamily / Phosphopantetheine attachment site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Predicted gene, 55359 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein bL9m ...FE2/S2 (INORGANIC) CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Predicted gene, 55359 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein bL9m / rRNA methyltransferase 3, mitochondrial / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein mL48 / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein mL37 / Large ribosomal subunit protein mL66 / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein mL42 / Large ribosomal subunit protein mL54 / Large ribosomal subunit protein mL51 / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein mL63 / Large ribosomal subunit protein bL20m / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein mL41 / Acyl carrier protein, mitochondrial / Large ribosomal subunit protein mL64 / Probable ATP-dependent RNA helicase DDX28 / Mitochondrial assembly of ribosomal large subunit protein 1 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein mL65 / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein mL52 / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein mL53 / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein uL13m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein mL39 / Large ribosomal subunit protein mL40
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.63 Å
AuthorsSingh, V. / Rorbach, J. / Freyer, C. / Amunts, A. / Wredenberg, A.
Funding support Sweden, Denmark, 3items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Novo Nordisk Foundation Denmark
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Commun / Year: 2025
Title: The mitochondrial methylation potential gates mitoribosome assembly.
Authors: Ruth I C Glasgow / Vivek Singh / Lucía Peña-Pérez / Alissa Wilhalm / Marco F Moedas / David Moore / Florian A Rosenberger / Xinping Li / Ilian Atanassov / Mira Saba / Miriam Cipullo / ...Authors: Ruth I C Glasgow / Vivek Singh / Lucía Peña-Pérez / Alissa Wilhalm / Marco F Moedas / David Moore / Florian A Rosenberger / Xinping Li / Ilian Atanassov / Mira Saba / Miriam Cipullo / Joanna Rorbach / Anna Wedell / Christoph Freyer / Alexey Amunts / Anna Wredenberg /
Abstract: S-adenosylmethionine (SAM) is the principal methyl donor in cells and is essential for mitochondrial gene expression, influencing RNA modifications, translation, and ribosome biogenesis. Using direct ...S-adenosylmethionine (SAM) is the principal methyl donor in cells and is essential for mitochondrial gene expression, influencing RNA modifications, translation, and ribosome biogenesis. Using direct long-read RNA sequencing in mouse tissues and embryonic fibroblasts, we show that processing of the mitochondrial ribosomal gene cluster fails in the absence of mitochondrial SAM, leading to an accumulation of unprocessed precursors. Proteomic analysis of ribosome fractions revealed these precursors associated with processing and assembly factors, indicating stalled biogenesis. Structural analysis by cryo-electron microscopy demonstrated that SAM-dependent methylation is required for peptidyl transferase centre formation during mitoribosome assembly. Our findings identify a critical role for SAM in coordinating mitoribosomal RNA processing and large subunit maturation, linking cellular methylation potential to mitochondrial translation capacity.
History
DepositionNov 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_related
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 / _em_admin.last_update
Revision 1.2Jul 16, 2025Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 16S rRNA (1584-MER)
B: tRNA-Phe (68-MER)
D: Large ribosomal subunit protein uL2m
E: Large ribosomal subunit protein uL3m
F: Large ribosomal subunit protein uL4m
H: Large ribosomal subunit protein bL9m
I: Large ribosomal subunit protein uL10m
J: Large ribosomal subunit protein uL11m
K: Large ribosomal subunit protein uL13m
L: Large ribosomal subunit protein uL14m
M: Large ribosomal subunit protein uL15m
N: Large ribosomal subunit protein uL16m
O: Large ribosomal subunit protein bL17m
P: Large ribosomal subunit protein uL18m
Q: Large ribosomal subunit protein bL19m
R: Large ribosomal subunit protein bL20m
S: Large ribosomal subunit protein bL21m
T: Large ribosomal subunit protein uL22m
U: Large ribosomal subunit protein uL23m
V: Large ribosomal subunit protein uL24m
X: Large ribosomal subunit protein bL28m,Large ribosomal subunit protein bL32m
Y: Large ribosomal subunit protein uL29m
Z: Large ribosomal subunit protein uL30m
0: Large ribosomal subunit protein bL32m
5: Large ribosomal subunit protein mL37
6: Large ribosomal subunit protein mL38
7: Large ribosomal subunit protein mL39
8: Large ribosomal subunit protein mL40
9: Large ribosomal subunit protein mL41
a: Large ribosomal subunit protein mL42
b: Large ribosomal subunit protein mL43
c: Large ribosomal subunit protein mL44
d: Large ribosomal subunit protein mL45
e: Large ribosomal subunit protein mL46
f: Large ribosomal subunit protein mL48
g: Large ribosomal subunit protein mL49
h: Large ribosomal subunit protein mL50
i: Large ribosomal subunit protein mL51
j: Large ribosomal subunit protein mL52
k: Large ribosomal subunit protein mL53
l: Large ribosomal subunit protein mL54
o: Large ribosomal subunit protein mL63
p: Large ribosomal subunit protein mL62
q: Large ribosomal subunit protein mL64
r: Large ribosomal subunit protein mL66
s: Large ribosomal subunit protein mL65
u: Mitochondrial assembly of ribosomal large subunit protein 1
v: Predicted gene, 55359
w: Acyl carrier protein, mitochondrial
x: rRNA methyltransferase 3, mitochondrial
y: rRNA methyltransferase 3, mitochondrial
z: Probable ATP-dependent RNA helicase DDX28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,862,48054
Polymers1,862,23952
Non-polymers2412
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 16S rRNA (1584-MER)


Mass: 508601.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 10336604
#2: RNA chain tRNA-Phe (68-MER)


Mass: 21862.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 10336604

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Large ribosomal subunit protein ... , 44 types, 44 molecules DEFHIJKLMNOPQRSTUVXYZ056789abc...

#3: Protein Large ribosomal subunit protein uL2m / 39S ribosomal protein L2 / mitochondrial / L2mt / MRP-L2


Mass: 27168.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D773
#4: Protein Large ribosomal subunit protein uL3m / 39S ribosomal protein L3 / mitochondrial / L3mt / MRP-L3


Mass: 39170.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99N95
#5: Protein Large ribosomal subunit protein uL4m / 39S ribosomal protein L4 / mitochondrial / L4mt / MRP-L4


Mass: 33120.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DCU6
#6: Protein Large ribosomal subunit protein bL9m / 39S ribosomal protein L9 / mitochondrial


Mass: 30896.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3UK02
#7: Protein Large ribosomal subunit protein uL10m / 39S ribosomal protein L10 / mitochondrial / L10mt / MRP-L10


Mass: 29438.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3TBW2
#8: Protein Large ribosomal subunit protein uL11m / 39S ribosomal protein L11 / mitochondrial / L11mt / MRP-L11


Mass: 20714.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQF0
#9: Protein Large ribosomal subunit protein uL13m / 39S ribosomal protein L13 / mitochondrial / L13mt / MRP-L13


Mass: 20707.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1P0
#10: Protein Large ribosomal subunit protein uL14m / 39S ribosomal protein L14 / mitochondrial / L14mt / MRP-L14


Mass: 15900.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1I6
#11: Protein Large ribosomal subunit protein uL15m / 39S ribosomal protein L15 / mitochondrial / L15mt / MRP-L15


Mass: 33595.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPR5
#12: Protein Large ribosomal subunit protein uL16m / 39S ribosomal protein L16 / mitochondrial / L16mt / MRP-L16


Mass: 28850.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99N93
#13: Protein Large ribosomal subunit protein bL17m / 39S ribosomal protein L17 / mitochondrial / L17mt / MRP-L17


Mass: 20282.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D8P4
#14: Protein Large ribosomal subunit protein uL18m / 39S ribosomal protein L18 / mitochondrial / L18mt / MRP-L18


Mass: 20707.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQL5
#15: Protein Large ribosomal subunit protein bL19m / 39S ribosomal protein L19 / mitochondrial / L19mt / MRP-L19


Mass: 33628.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D338
#16: Protein Large ribosomal subunit protein bL20m / 39S ribosomal protein L20 / mitochondrial / L20mt / MRP-L20


Mass: 17631.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQL4
#17: Protein Large ribosomal subunit protein bL21m / 39S ribosomal protein L21 / mitochondrial / L21mt / MRP-L21


Mass: 23401.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1N9
#18: Protein Large ribosomal subunit protein uL22m / 39S ribosomal protein L22 / mitochondrial / L22mt / MRP-L22


Mass: 23847.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BU88
#19: Protein Large ribosomal subunit protein uL23m / 39S ribosomal protein L23 / mitochondrial / L23mt / MRP-L23 / L23 mitochondrial-related protein


Mass: 17145.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O35972
#20: Protein Large ribosomal subunit protein uL24m / 39S ribosomal protein L24 / mitochondrial / L24mt / MRP-L24


Mass: 24986.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ06
#21: Protein Large ribosomal subunit protein bL28m,Large ribosomal subunit protein bL32m / 39S ribosomal protein L28 / mitochondrial / L28mt / MRP-L28 / 39S ribosomal protein L32 / ...39S ribosomal protein L28 / mitochondrial / L28mt / MRP-L28 / 39S ribosomal protein L32 / mitochondrial / L32mt / MRP-L32 / Heart-expressed gene 1 protein


Mass: 34560.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1B9, UniProt: Q9DCI9
#22: Protein Large ribosomal subunit protein uL29m / 39S ribosomal protein L47 / mitochondrial / L47mt / MRP-L47


Mass: 29786.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K2Y7
#23: Protein Large ribosomal subunit protein uL30m / 39S ribosomal protein L30 / mitochondrial / L30mt / MRP-L30


Mass: 18380.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D7N6
#24: Protein Large ribosomal subunit protein bL32m / 39S ribosomal protein L32 / mitochondrial / L32mt / MRP-L32 / Heart-expressed gene 1 protein


Mass: 21766.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DCI9
#25: Protein Large ribosomal subunit protein mL37 / 39S ribosomal protein L37 / mitochondrial / L37mt / MRP-L37


Mass: 48407.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q921S7
#26: Protein Large ribosomal subunit protein mL38 / 39S ribosomal protein L38 / mitochondrial / L38mt / MRP-L38


Mass: 45099.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K2M0
#27: Protein Large ribosomal subunit protein mL39 / 39S ribosomal protein L39 / mitochondrial / L39mt / MRP-L39


Mass: 38603.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9JKF7
#28: Protein Large ribosomal subunit protein mL40 / 39S ribosomal protein L40 / mitochondrial / L40mt / MRP-L40 / Nuclear localization signal- ...39S ribosomal protein L40 / mitochondrial / L40mt / MRP-L40 / Nuclear localization signal-containing protein deleted in velocardiofacial syndrome homolog


Mass: 24347.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9Z2Q5
#29: Protein Large ribosomal subunit protein mL41 / 39S ribosomal protein L41 / mitochondrial / L41mt / MRP-L41


Mass: 15284.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQN7
#30: Protein Large ribosomal subunit protein mL42 / 28S ribosomal protein S32 / mitochondrial / MRP-S32 / S32mt / 39S ribosomal protein L31 / L31mt / ...28S ribosomal protein S32 / mitochondrial / MRP-S32 / S32mt / 39S ribosomal protein L31 / L31mt / MRP-L31 / 39S ribosomal protein L42 / L42mt / MRP-L42


Mass: 16521.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPV3
#31: Protein Large ribosomal subunit protein mL43


Mass: 17905.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5RL20
#32: Protein Large ribosomal subunit protein mL44 / 39S ribosomal protein L44 / mitochondrial / L44mt / MRP-L44


Mass: 34912.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9CY73, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#33: Protein Large ribosomal subunit protein mL45 / 39S ribosomal protein L45 / mitochondrial / L45mt / MRP-L45


Mass: 35463.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0Q7
#34: Protein Large ribosomal subunit protein mL46 / 39S ribosomal protein L46 / mitochondrial / L46mt / MRP-L46


Mass: 32175.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9EQI8
#35: Protein Large ribosomal subunit protein mL48 / 39S ribosomal protein L48 / mitochondrial / L48mt / MRP-L48


Mass: 23989.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8JZS9
#36: Protein Large ribosomal subunit protein mL49 / 39S ribosomal protein L49 / mitochondrial / L49mt / MRP-L49


Mass: 19161.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQ40
#37: Protein Large ribosomal subunit protein mL50 / 39S ribosomal protein L50 / mitochondrial / L50mt / MRP-L50


Mass: 18241.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8VDT9
#38: Protein Large ribosomal subunit protein mL51 / 39S ribosomal protein L51 / mitochondrial / L51mt / MRP-L51 / bMRP-64 / bMRP64


Mass: 15132.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPY1
#39: Protein Large ribosomal subunit protein mL52 / 39S ribosomal protein L52 / mitochondrial / L52mt / MRP-L52


Mass: 13681.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0Y8
#40: Protein Large ribosomal subunit protein mL53 / 39S ribosomal protein L53 / mitochondrial / L53mt / MRP-L53


Mass: 12756.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1H8
#41: Protein Large ribosomal subunit protein mL54 / 39S ribosomal protein L54 / mitochondrial / L54mt / MRP-L54


Mass: 15450.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPW3
#42: Protein Large ribosomal subunit protein mL63 / Mitochondrial ribosomal protein 63 / Mitochondrial ribosomal protein L57 / Ribosomal protein 63 / ...Mitochondrial ribosomal protein 63 / Mitochondrial ribosomal protein L57 / Ribosomal protein 63 / mitochondrial / mMRP63


Mass: 11974.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQF8
#43: Protein Large ribosomal subunit protein mL62 / 39S ribosomal protein L58 / mitochondrial / MRP-L58 / Immature colon carcinoma transcript 1 protein ...39S ribosomal protein L58 / mitochondrial / MRP-L58 / Immature colon carcinoma transcript 1 protein homolog / Peptidyl-tRNA hydrolase ICT1


Mass: 23519.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8R035, peptidyl-tRNA hydrolase
#44: Protein Large ribosomal subunit protein mL64 / 39S ribosomal protein L59 / mitochondrial / MRP-L59 / Growth arrest and DNA damage-inducible ...39S ribosomal protein L59 / mitochondrial / MRP-L59 / Growth arrest and DNA damage-inducible proteins-interacting protein 1


Mass: 25865.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR59
#45: Protein Large ribosomal subunit protein mL66 / 28S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / 28S ribosomal protein S18a / MRP-S18-a / ...28S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / 28S ribosomal protein S18a / MRP-S18-a / Mrps18a / S18mt-a


Mass: 22363.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99N85
#46: Protein Large ribosomal subunit protein mL65 / 28S ribosomal protein S30 / mitochondrial / MRP-S30 / S30mt


Mass: 50005.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0G0

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Protein , 5 types, 6 molecules uvwxyz

#47: Protein Mitochondrial assembly of ribosomal large subunit protein 1


Mass: 26055.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWV0
#48: Protein Predicted gene, 55359


Mass: 8444.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0A2I3BQS8
#49: Protein Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 17390.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR21
#50: Protein rRNA methyltransferase 3, mitochondrial / 16S rRNA (guanosine(1370)-2'-O)-methyltransferase / 16S rRNA [Gm1370] 2'-O-methyltransferase / RNA ...16S rRNA (guanosine(1370)-2'-O)-methyltransferase / 16S rRNA [Gm1370] 2'-O-methyltransferase / RNA methyltransferase-like protein 1


Mass: 46868.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q5ND52, Transferases; Transferring one-carbon groups; Methyltransferases
#51: Protein Probable ATP-dependent RNA helicase DDX28 / Mitochondrial DEAD box protein 28


Mass: 59592.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWT6, RNA helicase

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Non-polymers , 2 types, 2 molecules

#52: Chemical ChemComp-ZN / ZINC ION


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


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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Details

Has ligand of interestN
Has protein modificationN

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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 the mitoribosome large subunit
Type: RIBOSOME / Entity ID: #24-#29, #1-#23, #30-#51 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8965 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00299359
ELECTRON MICROSCOPYf_angle_d0.396140103
ELECTRON MICROSCOPYf_dihedral_angle_d14.8923620
ELECTRON MICROSCOPYf_chiral_restr0.03316393
ELECTRON MICROSCOPYf_plane_restr0.00313579

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