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- PDB-7oic: Cryo-EM structure of late human 39S mitoribosome assembly interme... -

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Basic information

Entry
Database: PDB / ID: 7oic
TitleCryo-EM structure of late human 39S mitoribosome assembly intermediates, state 4
Components
  • (Large ribosomal subunit protein ...) x 49
  • 16S rRNA
  • 39S ribosomal protein L45, mitochondrial
  • 5-cytosine rRNA methyltransferase NSUN4
  • Acyl carrier protein, mitochondrial
  • MIEF1 upstream open reading frame protein
  • Mitochondrial assembly of ribosomal large subunit protein 1
  • RNA pCpA
  • Transcription termination factor 4, mitochondrial
  • mitochondrial Val tRNA
KeywordsRIBOSOME / 39S mitoribosome / ribosome biogenesis
Function / homology
Function and homology information


mRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / mitochondrial RNA modification / mitochondrial RNA catabolic process / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / Complex I biogenesis / protein lipoylation ...mRNA (cytidine-5-)-methyltransferase activity / rRNA modification in the mitochondrion / mitochondrial RNA modification / mitochondrial RNA catabolic process / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / Complex I biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / positive regulation of mitochondrial translation / RNA methyltransferase activity / Respiratory electron transport / rRNA import into mitochondrion / rRNA methyltransferase activity / mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / translation release factor activity / camera-type eye development / iron-sulfur cluster assembly complex / mitochondrial fission / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial large ribosomal subunit binding / mitochondrial ribosome / mitochondrial [2Fe-2S] assembly complex / mitochondrial small ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase activity / rRNA methylation / mitochondrial translation / [2Fe-2S] cluster assembly / : / iron-sulfur cluster assembly / acyl binding / ribosomal large subunit binding / acyl carrier activity / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled cytosolic ribosome / aerobic respiration / Transferases; Transferring one-carbon groups; Methyltransferases / fatty acid binding / cellular response to leukemia inhibitory factor / ribosomal large subunit biogenesis / methyltransferase activity / mitochondrial membrane / fibrillar center / rRNA processing / fatty acid biosynthetic process / cell junction / double-stranded RNA binding / heart development / 5S rRNA binding / double-stranded DNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / negative regulation of translation / mitochondrial inner membrane / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / apoptotic process / calcium ion binding / regulation of DNA-templated transcription / nucleolus / structural molecule activity / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
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 / : ...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. / : / 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 / Ribosomal protein L28/L40, mitochondrial / : / Mitochondrial ribosomal protein L28 / 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 / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / : / Beta-grasp domain superfamily / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NTF2-like domain superfamily / Acyl carrier protein (ACP) / NUDIX hydrolase-like domain superfamily / Ribosomal protein L11, bacterial-type / Nucleotidyltransferase superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P
Similarity search - Domain/homology
4'-PHOSPHOPANTETHEINE / S-ADENOSYLMETHIONINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Mitochondrial ribosome and complex I assembly factor AltMIEF1 / Acyl carrier protein, mitochondrial / Large ribosomal subunit protein bL33m ...4'-PHOSPHOPANTETHEINE / S-ADENOSYLMETHIONINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Mitochondrial ribosome and complex I assembly factor AltMIEF1 / Acyl carrier protein, mitochondrial / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein mL51 / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein mL54 / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein bL21m / Transcription termination factor 4, mitochondrial / Large ribosomal subunit protein mL55 / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein mL52 / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL64 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein uL24m / 5-cytosine rRNA methyltransferase NSUN4 / Large ribosomal subunit protein mL38 / Mitochondrial assembly of ribosomal large subunit protein 1 / Large ribosomal subunit protein mL53 / Large ribosomal subunit protein mL48 / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein mL63 / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL20m / Large ribosomal subunit protein uL13m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein mL37 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein mL65 / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein mL66 / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein mL39 / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein bL36m / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein mL42
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsCheng, J. / Berninghausen, O. / Beckmann, R.
CitationJournal: Nat Commun / Year: 2021
Title: A distinct assembly pathway of the human 39S late pre-mitoribosome.
Authors: Jingdong Cheng / Otto Berninghausen / Roland Beckmann /
Abstract: Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. ...Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.
History
DepositionMay 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
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Structure visualization

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Assembly

Deposited unit
A: 16S rRNA
B: mitochondrial Val tRNA
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
W: Large ribosomal subunit protein bL27m
X: Large ribosomal subunit protein bL28m
Y: Large ribosomal subunit protein uL29m
Z: Large ribosomal subunit protein uL30m
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
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: 39S ribosomal protein L45, mitochondrial
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
m: Large ribosomal subunit protein mL55
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: MIEF1 upstream open reading frame protein
w: Acyl carrier protein, mitochondrial
x: 5-cytosine rRNA methyltransferase NSUN4
y: Transcription termination factor 4, mitochondrial
C: RNA pCpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,882,690139
Polymers1,879,89058
Non-polymers2,80081
Water00
1


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

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Components

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RNA chain , 3 types, 3 molecules ABC

#1: RNA chain 16S rRNA


Mass: 500043.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: RNA chain mitochondrial Val tRNA


Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1485738021
#58: RNA chain RNA pCpA


Mass: 589.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Large ribosomal subunit protein ... , 49 types, 49 molecules DEFHIJKLMNOPQRSTUVWXYZ01234567...

#3: Protein Large ribosomal subunit protein uL2m


Mass: 33355.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5T653
#4: Protein Large ribosomal subunit protein uL3m


Mass: 38689.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09001
#5: Protein Large ribosomal subunit protein uL4m


Mass: 34970.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD3
#6: Protein Large ribosomal subunit protein bL9m


Mass: 30296.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD2
#7: Protein Large ribosomal subunit protein uL10m


Mass: 29322.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7H8
#8: Protein Large ribosomal subunit protein uL11m


Mass: 20716.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B7
#9: Protein Large ribosomal subunit protein uL13m


Mass: 20722.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD1
#10: Protein Large ribosomal subunit protein uL14m


Mass: 15973.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P1L8
#11: Protein Large ribosomal subunit protein uL15m


Mass: 33473.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P015
#12: Protein Large ribosomal subunit protein uL16m


Mass: 28496.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX20
#13: Protein Large ribosomal subunit protein bL17m


Mass: 20083.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRX2
#14: Protein Large ribosomal subunit protein uL18m


Mass: 20607.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H0U6
#15: Protein Large ribosomal subunit protein bL19m


Mass: 33584.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49406
#16: Protein Large ribosomal subunit protein bL20m


Mass: 17479.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC9
#17: Protein Large ribosomal subunit protein bL21m


Mass: 22847.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z2W9
#18: Protein Large ribosomal subunit protein uL22m


Mass: 23683.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWU5
#19: Protein Large ribosomal subunit protein uL23m


Mass: 17807.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16540
#20: Protein Large ribosomal subunit protein uL24m


Mass: 24953.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96A35
#21: Protein Large ribosomal subunit protein bL27m


Mass: 16102.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0M9
#22: Protein Large ribosomal subunit protein bL28m


Mass: 30090.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13084
#23: Protein Large ribosomal subunit protein uL29m


Mass: 29508.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HD33
#24: Protein Large ribosomal subunit protein uL30m


Mass: 18582.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TCC3
#25: Protein Large ribosomal subunit protein bL32m


Mass: 21437.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC8
#26: Protein Large ribosomal subunit protein bL33m


Mass: 7635.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75394
#27: Protein Large ribosomal subunit protein bL34m


Mass: 10183.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQ48
#28: Protein Large ribosomal subunit protein bL35m


Mass: 21558.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NZE8
#29: Protein Large ribosomal subunit protein bL36m


Mass: 11809.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0J6
#30: Protein Large ribosomal subunit protein mL37


Mass: 48183.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZE1
#31: Protein Large ribosomal subunit protein mL38


Mass: 44659.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DV4
#32: Protein Large ribosomal subunit protein mL39


Mass: 38764.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NYK5
#33: Protein Large ribosomal subunit protein mL40


Mass: 24534.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NQ50
#34: Protein Large ribosomal subunit protein mL41


Mass: 15404.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8IXM3
#35: Protein Large ribosomal subunit protein mL42


Mass: 16691.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6G3
#36: Protein Large ribosomal subunit protein mL43


Mass: 23457.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N983
#37: Protein Large ribosomal subunit protein mL44


Mass: 37583.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H9J2
#39: Protein Large ribosomal subunit protein mL46


Mass: 31748.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H2W6
#40: Protein Large ribosomal subunit protein mL48


Mass: 23970.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96GC5
#41: Protein Large ribosomal subunit protein mL49


Mass: 19225.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13405
#42: Protein Large ribosomal subunit protein mL50


Mass: 18349.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N5N7
#43: Protein Large ribosomal subunit protein mL51


Mass: 15125.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q4U2R6
#44: Protein Large ribosomal subunit protein mL52


Mass: 13682.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86TS9
#45: Protein Large ribosomal subunit protein mL53


Mass: 12125.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EL3
#46: Protein Large ribosomal subunit protein mL54


Mass: 15844.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P161
#47: Protein Large ribosomal subunit protein mL55


Mass: 15160.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7F7
#48: Protein Large ribosomal subunit protein mL63


Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6
#49: Protein Large ribosomal subunit protein mL62


Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14197
#50: Protein Large ribosomal subunit protein mL64


Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8
#51: Protein Large ribosomal subunit protein mL66


Mass: 22224.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NVS2
#52: Protein Large ribosomal subunit protein mL65


Mass: 50429.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NP92

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Protein , 6 types, 6 molecules duvwxy

#38: Protein 39S ribosomal protein L45, mitochondrial / MRP-L45 / Mitochondrial large ribosomal subunit protein mL45


Mass: 35402.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRJ2
#53: Protein Mitochondrial assembly of ribosomal large subunit protein 1


Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EH3
#54: Protein MIEF1 upstream open reading frame protein


Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8
#55: Protein Acyl carrier protein, mitochondrial


Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561
#56: Protein 5-cytosine rRNA methyltransferase NSUN4


Mass: 43187.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96CB9
#57: Protein Transcription termination factor 4, mitochondrial


Mass: 44012.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z6M4

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Non-polymers , 4 types, 81 molecules

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


Mass: 24.305 Da / Num. of mol.: 76 / Source method: obtained synthetically / Formula: Mg
#60: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#61: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#62: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S

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Details

Has ligand of interestN
Has protein modificationY

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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: Human 39S mitoribosome assembly intermediates, state 4
Type: RIBOSOME / Entity ID: #1-#57 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
4CTFFINDCTF correction
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83176 / Symmetry type: POINT

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