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- PDB-7pkt: Large subunit of the Chlamydomonas reinhardtii mitoribosome -

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Basic information

Entry
Database: PDB / ID: 7pkt
TitleLarge subunit of the Chlamydomonas reinhardtii mitoribosome
Components
  • (50S ribosomal protein ...) x 2
  • (Mitochondrial ribosomal protein ...) x 6
  • KOW domain-containing protein,uL24m
  • L1 rRNA
  • L2a rRNA
  • L3a rRNA (5S)
  • L3b rRNA
  • L4 rRNA
  • L5 rRNA
  • L6 rRNA
  • L7 rRNA
  • L8 rRNA
  • PPR*
  • Plastid ribosomal protein L6
  • Ribosomal_L16 domain-containing protein
  • Ribosomal_L18e/L15P domain-containing protein
  • Ribosomal_L2_C domain-containing protein
  • Ribosomal_L30 domain-containing protein
  • Ribosomal_TL5_C domain-containing protein
  • Unk1
  • Unk2
  • bL21m
  • bL27m
  • bL28m
  • bL32m
  • bL34m
  • bL35m
  • bL36m
  • mL113
  • mL114
  • mL115
  • mL116
  • mL117
  • mL118
  • mL119
  • mL40
  • mL41
  • mL43
  • mL59/64
  • mL63/57/60
  • mL80
  • mL87
  • uL14m
  • uL22m
  • uL29m
  • uL3m
  • uL4m
  • uL5m
KeywordsRIBOSOME / Mitochondria / mitoribosome / alga
Function / homology
Function and homology information


chloroplast rRNA processing / regulation of mitochondrial mRNA stability / ribonucleoprotein granule / mitochondrial RNA processing / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / ribosome assembly / chloroplast / ribosomal large subunit assembly ...chloroplast rRNA processing / regulation of mitochondrial mRNA stability / ribonucleoprotein granule / mitochondrial RNA processing / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / ribosome assembly / chloroplast / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / translation / mRNA binding / mitochondrion / RNA binding / cytoplasm
Similarity search - Function
Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / 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) / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein/NADH dehydrogenase domain ...Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / 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) / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NUDIX hydrolase-like domain superfamily / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L17 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L6 / Ribosomal protein L2, domain 3 / Ribosomal protein L14P, conserved site / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Ribosomal protein L14 signature. / Ribosomal protein L15 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L30p/L7e / Ribosomal protein L23 / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L24 signature. / Ribosomal protein L14p/L23e / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal_L18e/L15P domain-containing protein ...FE2/S2 (INORGANIC) CLUSTER / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal_L18e/L15P domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / KOW domain-containing protein / Uncharacterized protein / Ribosomal_L2_C domain-containing protein / Ribosomal_L16 domain-containing protein / Uncharacterized protein / 50S ribosomal protein L9, chloroplastic / Uncharacterized protein / Ribosomal_L30 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal_TL5_C domain-containing protein / Uncharacterized protein / Uncharacterized protein / 50S ribosomal protein L20 / Predicted protein / Predicted protein / Predicted protein / Mitochondrial ribosomal protein L19 / Uncharacterized protein / Mitochondrial ribosomal protein L17 / Predicted protein / Predicted protein / Predicted protein / Plastid ribosomal protein L6 / Predicted protein / Mitochondrial ribosomal protein L23 / Mitochondrial ribosomal protein L13 / Mitochondrial ribosomal protein L33 / Predicted protein / Mitochondrial ribosomal protein L17
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWaltz, F. / Soufari, H. / Hashem, Y.
Funding supportEuropean Union, France, 4items
OrganizationGrant numberCountry
European Research Council (ERC)TransTryp ID:759120European Union
Agence Nationale de la Recherche (ANR)ANR-11-LABX-0057_MITOCROSS France
Agence Nationale de la Recherche (ANR)MITRA, ANR-16-CE11-0024-02 France
Agence Nationale de la Recherche (ANR)DAMIA, ANR-20-CE11-0021 France
CitationJournal: Nat Commun / Year: 2021
Title: How to build a ribosome from RNA fragments in Chlamydomonas mitochondria.
Authors: Florent Waltz / Thalia Salinas-Giegé / Robert Englmeier / Herrade Meichel / Heddy Soufari / Lauriane Kuhn / Stefan Pfeffer / Friedrich Förster / Benjamin D Engel / Philippe Giegé / ...Authors: Florent Waltz / Thalia Salinas-Giegé / Robert Englmeier / Herrade Meichel / Heddy Soufari / Lauriane Kuhn / Stefan Pfeffer / Friedrich Förster / Benjamin D Engel / Philippe Giegé / Laurence Drouard / Yaser Hashem /
Abstract: Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the ...Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the few essential messenger RNAs still encoded by mitochondrial genomes. Here, we present a biochemical and structural characterization of the mitoribosome in the model green alga Chlamydomonas reinhardtii, as well as a functional study of some of its specific components. Single particle cryo-electron microscopy resolves how the Chlamydomonas mitoribosome is assembled from 13 rRNA fragments encoded by separate non-contiguous gene pieces. Additional proteins, mainly OPR, PPR and mTERF helical repeat proteins, are found in Chlamydomonas mitoribosome, revealing the structure of an OPR protein in complex with its RNA binding partner. Targeted amiRNA silencing indicates that these ribosomal proteins are required for mitoribosome integrity. Finally, we use cryo-electron tomography to show that Chlamydomonas mitoribosomes are attached to the inner mitochondrial membrane via two contact points mediated by Chlamydomonas-specific proteins. Our study expands our understanding of mitoribosome diversity and the various strategies these specialized molecular machines adopt for membrane tethering.
History
DepositionAug 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: Ribosomal_L2_C domain-containing protein
b: uL3m
c: uL4m
d: uL5m
f: 50S ribosomal protein L9, chloroplastic
i: Mitochondrial ribosomal protein L13
j: uL14m
k: Ribosomal_L18e/L15P domain-containing protein
l: Ribosomal_L16 domain-containing protein
m: Mitochondrial ribosomal protein L17,bL17m
n: Mitochondrial ribosomal protein L19
o: 50S ribosomal protein L20
p: bL21m
q: uL22m
r: Mitochondrial ribosomal protein L23
s: KOW domain-containing protein,uL24m
t: Ribosomal_TL5_C domain-containing protein
u: bL27m
v: bL28m
w: uL29m
x: Ribosomal_L30 domain-containing protein
y: bL32m
z: Mitochondrial ribosomal protein L33
A: bL34m
B: bL35m
e: Plastid ribosomal protein L6
D: mL40
E: mL41
F: mL43
G: Mitochondrial ribosomal protein L17
I: mL63/57/60
J: mL59/64
K: mL80
L: mL87
C: bL36m
M: mL113
N: mL114
O: mL115
P: mL116
Q: mL117
R: mL118
S: mL119
X: Unk1
Y: PPR*
Z: Unk2
1: L1 rRNA
2: L2a rRNA
0: L3a rRNA (5S)
3: L3b rRNA
4: L4 rRNA
5: L5 rRNA
6: L6 rRNA
7: L7 rRNA
8: L8 rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,926,381125
Polymers1,924,46354
Non-polymers1,91871
Water0
1


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

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Components

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Protein , 34 types, 34 molecules abcdjklpqstuvwxyABeDEFIJKLMNOP...

#1: Protein Ribosomal_L2_C domain-containing protein


Mass: 41087.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DL58
#2: Protein uL3m


Mass: 44936.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E681
#3: Protein uL4m


Mass: 45910.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D422
#4: Protein uL5m


Mass: 23054.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DYN2
#7: Protein uL14m


Mass: 13356.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IYH4
#8: Protein Ribosomal_L18e/L15P domain-containing protein


Mass: 35532.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D8F3
#9: Protein Ribosomal_L16 domain-containing protein


Mass: 27922.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DP67
#13: Protein bL21m


Mass: 40170.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DDN8
#14: Protein uL22m


Mass: 39180.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DSG6
#16: Protein KOW domain-containing protein,uL24m


Mass: 31164.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DJU3
#17: Protein Ribosomal_TL5_C domain-containing protein


Mass: 38730.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E0K7
#18: Protein bL27m


Mass: 18010.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: N-ter is extend compared to A0A2K3E880,N-ter is extend compared to A0A2K3E880,N-ter is extend compared to A0A2K3E880,N-ter is extend compared to A0A2K3E880
Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E880
#19: Protein bL28m


Mass: 17000.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D077
#20: Protein uL29m


Mass: 14799.233 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HUW1
#21: Protein Ribosomal_L30 domain-containing protein


Mass: 24367.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DSP9
#22: Protein bL32m


Mass: 13370.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JGW4
#24: Protein bL34m


Mass: 29646.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CX36
#25: Protein bL35m


Mass: 17493.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DKX8
#26: Protein Plastid ribosomal protein L6


Mass: 22275.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J503
#27: Protein mL40


Mass: 17749.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D9N2
#28: Protein mL41


Mass: 12623.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J2J1
#29: Protein mL43


Mass: 16217.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HW20
#31: Protein mL63/57/60


Mass: 14645.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IS96
#32: Protein mL59/64


Mass: 14372.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HPK3
#33: Protein mL80


Mass: 27176.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DBX4
#34: Protein mL87


Mass: 23535.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J535
#36: Protein mL113


Mass: 84437.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DVD3
#37: Protein mL114


Mass: 48757.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DR53
#38: Protein mL115


Mass: 72344.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J070
#39: Protein mL116


Mass: 53018.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DXQ3
#40: Protein mL117


Mass: 75804.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CXJ4
#41: Protein mL118


Mass: 64122.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DTE5
#42: Protein mL119


Mass: 36808.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D424
#44: Protein PPR*


Mass: 14656.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)

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50S ribosomal protein ... , 2 types, 2 molecules fo

#5: Protein 50S ribosomal protein L9, chloroplastic / Ribosome / CL9


Mass: 30622.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DRF9
#12: Protein 50S ribosomal protein L20 /


Mass: 13140.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HNL1

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Mitochondrial ribosomal protein ... , 6 types, 6 molecules imnrzG

#6: Protein Mitochondrial ribosomal protein L13


Mass: 29714.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J810
#10: Protein Mitochondrial ribosomal protein L17,bL17m


Mass: 21380.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein is a mixture of A0A2K3DXS2 and A8JH49,The protein is a mixture of A0A2K3DXS2 and A8JH49
Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JH49, UniProt: A0A2K3DXS2
#11: Protein Mitochondrial ribosomal protein L19


Mass: 33412.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I7A8
#15: Protein Mitochondrial ribosomal protein L23


Mass: 25593.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J6R9
#23: Protein Mitochondrial ribosomal protein L33


Mass: 6864.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J9C3
#30: Protein Mitochondrial ribosomal protein L17


Mass: 27320.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IWI1

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Protein/peptide , 3 types, 3 molecules CXZ

#35: Protein/peptide bL36m


Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#43: Protein/peptide Unk1


Mass: 2656.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#45: Protein/peptide Unk2


Mass: 4188.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)

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RNA chain , 9 types, 9 molecules 120345678

#46: RNA chain L1 rRNA


Mass: 51976.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#47: RNA chain L2a rRNA


Mass: 27512.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#48: RNA chain L3a rRNA (5S)


Mass: 24033.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#49: RNA chain L3b rRNA


Mass: 59395.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#50: RNA chain L4 rRNA


Mass: 38253.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#51: RNA chain L5 rRNA


Mass: 47720.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#52: RNA chain L6 rRNA


Mass: 43923.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#53: RNA chain L7 rRNA


Mass: 186482.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#54: RNA chain L8 rRNA


Mass: 132907.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)

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Non-polymers , 3 types, 71 molecules

#55: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 69 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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

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Details

Has ligand of interestN

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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: Large subunit of the mitochondrial ribosome of Chlamydomonas reinhardtii
Type: RIBOSOME / Entity ID: #1-#54 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organelle: Mitochondria
Buffer solutionpH: 7.6
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 65

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2SerialEMimage acquisition
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101291 / Num. of class averages: 2 / Symmetry type: POINT

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