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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 / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial translational termination / mitochondrial genome maintenance / mitochondrial translational elongation / ribonuclease III activity / translation release factor activity, codon nonspecific / Mitochondrial protein degradation / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit / mitochondrial fission / mitochondrial large ribosomal subunit binding / peptidyl-tRNA hydrolase / mitochondrial ribosome / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial small ribosomal subunit / peptidyl-tRNA hydrolase activity / [2Fe-2S] cluster assembly / mitochondrial translation / iron-sulfur cluster assembly / mitochondrial nucleoid / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / respiratory chain complex I / RNA processing / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / aerobic respiration / Transferases; Transferring one-carbon groups; Methyltransferases / ribosomal large subunit biogenesis / fatty acid biosynthetic process / cell junction / double-stranded RNA binding / 5S rRNA binding / mitochondrial inner membrane / RNA helicase activity / rRNA binding / nuclear body / RNA helicase / structural constituent of ribosome / mitochondrial matrix / protein domain specific binding / translation / ribonucleoprotein complex / nucleotide binding / apoptotic process / nucleolus / 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 / 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 / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 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 / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Ribonuclease III, endonuclease domain superfamily / 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 / Acyl carrier protein (ACP) / NTF2-like domain superfamily / 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 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Phosphopantetheine attachment site / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal
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 early and late ribosome assembly
Authors: Glasgow, R. / Singh, V. / Pena-Perez, L. / Wilhalm, A. / Moedas, M.F. / Moore, D. / Rosenberger, F.A. / Li, X. / Atanassov, I. / Saba, M. / Cipullo, M. / Rorbach, J. / Wedell, A. / Freyer, C. ...Authors: Glasgow, R. / Singh, V. / Pena-Perez, L. / Wilhalm, A. / Moedas, M.F. / Moore, D. / Rosenberger, F.A. / Li, X. / Atanassov, I. / Saba, M. / Cipullo, M. / Rorbach, J. / Wedell, A. / Freyer, C. / Amunts, A. / Wredenberg, A.
History
DepositionNov 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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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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