[English] 日本語
Yorodumi
- PDB-9e9c: Mouse mitoribosome large subunit assembly intermediate bound to N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9e9c
TitleMouse mitoribosome large subunit assembly intermediate bound to NSUN4, METRF4, GTPBP7, GTPBP10 and the MALSU1-L0R8F8-mt-ACP complex (without uL16m), State B1 (SAMC knock-out)
Components
  • (Large ribosomal subunit protein ...) x 49
  • (Mitochondrial ...) x 2
  • 5-cytosine rRNA methyltransferase NSUN4
  • Acyl carrier protein, mitochondrial
  • GTP-binding protein 10
  • Predicted gene, 55359
  • RNA (1428-MER)
  • RNA (56-MER)
  • Transcription termination factor 4, mitochondrial
KeywordsRIBOSOME / mitochondria / ribosome assembly / large subunit
Function / homology
Function and homology information


Mitochondrial translation elongation / mRNA (cytidine-5-)-methyltransferase activity / regulation of respiratory system process / mitochondrial small ribosomal subunit assembly / mitochondrial RNA catabolic process / regulation of mitochondrial translation / negative regulation of mitochondrial translation / regulation of mitochondrial transcription / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis ...Mitochondrial translation elongation / mRNA (cytidine-5-)-methyltransferase activity / regulation of respiratory system process / mitochondrial small ribosomal subunit assembly / mitochondrial RNA catabolic process / regulation of mitochondrial translation / negative regulation of mitochondrial translation / regulation of mitochondrial transcription / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / positive regulation of mitochondrial translation / Mitochondrial ribosome-associated quality control / mitochondrial large ribosomal subunit assembly / Mitochondrial translation termination / Respiratory electron transport / translation release factor activity / rRNA import into mitochondrion / mitochondrial translational termination / ribonuclease III activity / mitochondrial translational elongation / mitochondrial ribosome assembly / Mitochondrial protein degradation / translation release factor activity, codon nonspecific / camera-type eye development / protein lipoylation / mitochondrial fission / iron-sulfur cluster assembly complex / peptidyl-tRNA hydrolase / mitochondrial large ribosomal subunit / mitochondrial large ribosomal subunit binding / mitochondrial [2Fe-2S] assembly complex / mitochondrial ribosome / rRNA methylation / mitochondrial small ribosomal subunit / peptidyl-tRNA hydrolase activity / mitochondrial translation / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / ribosomal large subunit binding / proton motive force-driven mitochondrial ATP synthesis / acyl binding / mitochondrial respiratory chain complex I assembly / respiratory chain complex I / acyl carrier activity / RNA processing / cytosolic ribosome / rescue of stalled cytosolic ribosome / Transferases; Transferring one-carbon groups; Methyltransferases / aerobic respiration / cellular response to leukemia inhibitory factor / ribosomal large subunit biogenesis / mitochondrion organization / fibrillar center / rRNA processing / cell junction / double-stranded RNA binding / large ribosomal subunit / heart development / ribosome biogenesis / 5S rRNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / mitochondrial inner membrane / negative regulation of translation / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / GTPase activity / apoptotic process / GTP binding / nucleolus / structural molecule activity / magnesium ion binding / mitochondrion / RNA binding / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
GTPase, MTG1 / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / OBG-type GTPase / GTP1/OBG / Obg domain profile. / Mitochondrial termination factor repeats / Transcription termination factor, mitochondrial/chloroplastic / MTERF superfamily, mitochondrial/chloroplastic ...GTPase, MTG1 / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / OBG-type GTPase / GTP1/OBG / Obg domain profile. / Mitochondrial termination factor repeats / Transcription termination factor, mitochondrial/chloroplastic / MTERF superfamily, mitochondrial/chloroplastic / mTERF / MIEF1-MP, LYR domain / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / : / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / GTP-binding protein, orthogonal bundle domain superfamily / : / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / : / Mitochondrial ribosomal protein L55 / 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 / Mitochondrial ribosomal protein L37 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L35, mitochondrial / 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 / : / : / Large ribosomal subunit protein mL44, endonuclease domain / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / : / : / 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 L50, mitochondria / MRPL44, double-stranded RNA binding domain / Ribosomal subunit 39S / MRPL44 dsRNA-binding domain / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / : / Mitochondrial ribosomal protein L27 / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / 39S ribosomal protein L46, mitochondrial / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / 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 / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / 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 / 50S ribosome-binding GTPase / Ribonuclease III, endonuclease domain superfamily / GTP binding domain / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Complex 1 LYR protein domain / Complex 1 protein (LYR family)
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Predicted gene, 55359 / Large ribosomal subunit protein uL23m ...FE2/S2 (INORGANIC) CLUSTER / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Predicted gene, 55359 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein uL22m / Transcription termination factor 4, mitochondrial / Large ribosomal subunit protein mL48 / GTP-binding protein 10 / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein mL62 / Mitochondrial ribosome-associated GTPase 1 / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein mL37 / Large ribosomal subunit protein mL66 / Large ribosomal subunit protein bL36m / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein bL9m / 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 bL35m / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein bL33m / Acyl carrier protein, mitochondrial / Large ribosomal subunit protein mL64 / Mitochondrial assembly of ribosomal large subunit protein 1 / Large ribosomal subunit protein mL44 / 5-cytosine rRNA methyltransferase NSUN4 / Large ribosomal subunit protein mL55 / 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: 3.62 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: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (1428-MER)
B: RNA (56-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
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
W: Large ribosomal subunit protein bL27m
X: Large ribosomal subunit protein bL28m
Y: Large ribosomal subunit protein uL29m
Z: Large ribosomal subunit protein uL30m
x: 5-cytosine rRNA methyltransferase NSUN4
0: Large ribosomal subunit protein bL32m
1: Large ribosomal subunit protein bL33m
2: Large ribosomal subunit protein bL34m
3: Large ribosomal subunit protein bL35m
4: Large ribosomal subunit protein bL36m
6: Large ribosomal subunit protein mL38
7: Large ribosomal subunit protein mL39
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
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
5: Large ribosomal subunit protein mL37
8: Large ribosomal subunit protein mL40
9: Large ribosomal subunit protein mL41
a: Large ribosomal subunit protein mL42
m: Large ribosomal subunit protein mL55
z: Mitochondrial ribosome-associated GTPase 1
l: Large ribosomal subunit protein mL54
y: Transcription termination factor 4, mitochondrial
t: GTP-binding protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,927,248158
Polymers1,923,58858
Non-polymers3,660100
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
RNA chain , 2 types, 2 molecules AB

#1: RNA chain RNA (1428-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 RNA (56-MER)


Mass: 21862.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 13103

+
Large ribosomal subunit protein ... , 49 types, 49 molecules DEFHIJKLMOPQRSTUVWXYZ0123467bc...

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


Mass: 33396.895 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 / L9mt / MRP-L9


Mass: 30298.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99N94
#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 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: Protein Large ribosomal subunit protein bL27m / 39S ribosomal protein L27 / mitochondrial / L27mt / MRP-L27


Mass: 15973.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99N92
#21: Protein Large ribosomal subunit protein bL28m / 39S ribosomal protein L28 / mitochondrial / L28mt / MRP-L28


Mass: 30221.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1B9
#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
#25: 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
#26: Protein Large ribosomal subunit protein bL33m / 39S ribosomal protein L33 / mitochondrial / L33mt / MRP-L33


Mass: 7431.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQP0
#27: Protein Large ribosomal subunit protein bL34m / 39S ribosomal protein L34 / mitochondrial / L34mt / MRP-L34


Mass: 10552.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99N91
#28: Protein Large ribosomal subunit protein bL35m / 39S ribosomal protein L35 / mitochondrial / L35mt / MRP-L35


Mass: 21546.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQL6
#29: Protein Large ribosomal subunit protein bL36m / 39S ribosomal protein L36 / mitochondrial / L36mt / MRP-L36


Mass: 11438.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99N90
#30: 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
#31: 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
#32: Protein Large ribosomal subunit protein mL43 / 39S ribosomal protein L43 / mitochondrial / Mitochondrial ribosomal protein bMRP36a


Mass: 17905.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5RL20
#33: 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
#34: 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
#35: 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
#36: 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
#37: 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
#38: 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
#39: 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
#40: 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
#41: 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
#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
#50: 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
#51: 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
#52: 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
#53: 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
#54: Protein Large ribosomal subunit protein mL55 / 39S ribosomal protein L55 / mitochondrial / L55mt / MRP-L55


Mass: 15152.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZ83
#56: 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

-
Protein , 5 types, 5 molecules xvwyt

#24: Protein 5-cytosine rRNA methyltransferase NSUN4 / 5-cytosine tRNA methyltransferase NSUN4 / NOL1/NOP2/Sun domain family member 4 / Sperm head and ...5-cytosine tRNA methyltransferase NSUN4 / NOL1/NOP2/Sun domain family member 4 / Sperm head and tail associated protein


Mass: 42904.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9CZ57, Transferases; Transferring one-carbon groups; Methyltransferases
#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
#57: Protein Transcription termination factor 4, mitochondrial / Mitochondrial transcription termination factor 4 / mTERF domain-containing protein 2


Mass: 40306.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BVN4
#58: Protein GTP-binding protein 10


Mass: 40200.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K013

-
Mitochondrial ... , 2 types, 2 molecules uz

#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
#55: Protein Mitochondrial ribosome-associated GTPase 1 / GTP-binding protein 7 / Mitochondrial GTPase 1


Mass: 36732.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8R2R6

-
Non-polymers , 4 types, 100 molecules

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


Mass: 24.305 Da / Num. of mol.: 95 / Source method: obtained synthetically / Formula: Mg
#60: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#61: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#62: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: mitoribosome large subunit assembly intermediate / Type: RIBOSOME
Entity ID: #1-#2, #24, #3-#6, #9-#23, #25-#54, #7, #55-#57, #8, #58
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

-
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)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6503 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002112208
ELECTRON MICROSCOPYf_angle_d0.438158809
ELECTRON MICROSCOPYf_dihedral_angle_d15.57928032
ELECTRON MICROSCOPYf_chiral_restr0.03418636
ELECTRON MICROSCOPYf_plane_restr0.00314880

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more