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- PDB-6ywy: The structure of the mitoribosome from Neurospora crassa with bou... -

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Basic information

Entry
Database: PDB / ID: 6ywy
TitleThe structure of the mitoribosome from Neurospora crassa with bound tRNA at the P-site
Components
  • (37S ribosomal protein ...) x 3
  • (54S ribosomal protein ...) x 2
  • (60S ribosomal protein ...) x 3
  • (L51_S25_CI-B8 domain-containing ...) x 2
  • (Mitochondrial ...) x 3
  • (Probable ribosomal protein ...) x 2
  • (Related to ribosomal protein ...) x 12
  • (Ribosomal protein ...) x 7
  • 16S rRNA
  • 23S rRNA
  • 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
  • 30S ribosomal protein S10, mitochondrial
  • DUF1713 domain-containing protein
  • IF1
  • KOW domain-containing protein
  • Manganese and iron superoxide dismutase
  • Mito ribosomal protein S2
  • Mitoc_mL59 domain-containing protein
  • P-site-tRNA
  • PEBP-like protein
  • Poly-Peptide
  • Protein FYV4, mitochondrial
  • RIBOSOMAL_L9 domain-containing protein
  • RNase III domain-containing protein
  • Related to 60s ribosomal protein L2 (Mitochondrial)
  • Ribonuclease III
  • Ribosomal protein
  • Ribosomal_S7 domain-containing protein
  • S4 RNA-binding domain-containing protein
  • Translational machinery component
  • bL19m
  • bL28m
  • bL33m
  • bS16m
  • bS1m
  • bS21m
  • mL40
  • mL41
  • mL46
  • mL49
  • mL50
  • mL54
  • mL67
  • mRNA
  • mS26
  • mS27
  • mS33
  • mS45
  • mS46
  • uL11m
  • uL13m
  • uL17m
  • uL23m
  • uL6m
  • uS17m
  • uS8m
  • uS9m
KeywordsTRANSLATION / Neurospora crassa / translating Mitoribosomes / tRNA / mRNA / mL108
Function / homology
Function and homology information


3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / L-valine catabolic process / DNA strand exchange activity / negative regulation of ATP-dependent activity / ribonuclease III activity / : / ATPase inhibitor activity / mitochondrial large ribosomal subunit / mitochondrial ribosome ...3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / L-valine catabolic process / DNA strand exchange activity / negative regulation of ATP-dependent activity / ribonuclease III activity / : / ATPase inhibitor activity / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / superoxide dismutase activity / positive regulation of proteolysis / RNA processing / rRNA processing / peroxisome / single-stranded DNA binding / double-stranded RNA binding / large ribosomal subunit / transferase activity / small ribosomal subunit / small ribosomal subunit rRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mitochondrion / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
54S ribosomal protein L44, mitochondrial / : / Ribosomal protein L31, mitochondrial / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L25 / 54S ribosomal protein L15, mitochondrial / MRPL25 domain / 54S ribosomal protein L28, mitochondrial / 54S ribosomal protein L3, double-stranded RNA binding domain ...54S ribosomal protein L44, mitochondrial / : / Ribosomal protein L31, mitochondrial / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L25 / 54S ribosomal protein L15, mitochondrial / MRPL25 domain / 54S ribosomal protein L28, mitochondrial / 54S ribosomal protein L3, double-stranded RNA binding domain / Mitochondrial ribosomal protein subunit L20 / Transcriptional regulation of mitochondrial recombination / Mitochondrial ribosomal protein mL59 / Mitochondrial ribosomal protein L31 / 54S ribosomal protein L36, yeast / : / Ribosomal protein L31p, N-terminal / Mitochondrial ribosomal protein MRP51, fungi / Mitochondrial ribosomal protein S25 / Ribosomal protein S24, mitochondrial / Ribosomal protein S23, mitochondrial, fungi / Mitochondrial ribosomal protein subunit / Mitochondrial ribosomal protein S25 / Ribosomal protein S35, mitochondrial / Ribosomal protein MRP10, mitochondrial / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Eukaryotic mitochondrial regulator protein / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / Small ribosomal subunit protein mS41 SAM domain / IGR protein motif / IGR / Ribonuclease-III-like / Ribonuclease III / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / 28S ribosomal protein S25, mitochondrial / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Ribosomal protein L37, mitochondrial / Mitochondrial ribosomal protein L37 / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / 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) / Mitochondrial mRNA-processing protein COX24, C-terminal / Ribosomal protein L27/L41, mitochondrial / : / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial ribosomal protein L27 / Mitochondrial domain of unknown function (DUF1713) / 39S ribosomal protein L46, mitochondrial / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / 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 / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double-stranded RNA-binding domain / : / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / ClpP/crotonase-like domain superfamily / Ribosomal protein L1, 3-layer alpha/beta-sandwich / NUDIX hydrolase-like domain superfamily / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Sterile alpha motif/pointed domain superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L10-like domain superfamily / Ribosomal protein L16 signature 2.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Mitochondrial 37S ribosomal protein MRP2 / ATP synthase F1 subunit epsilon ...ADENOSINE-5'-TRIPHOSPHATE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Mitochondrial 37S ribosomal protein MRP2 / ATP synthase F1 subunit epsilon / Nucleic acid-binding protein / 60S ribosomal protein L2, mitochondrial / 37S ribosomal protein mrp5 / RIBOSOMAL_L9 domain-containing protein / Ribosomal protein S16 / Ribosomal protein L15 / Manganese and iron superoxide dismutase / Large ribosomal subunit protein mL59 domain-containing protein / Mitochondrial 54S ribosomal protein YmL19 / 54S ribosomal protein L24 / Ribosomal protein S6 / Ribonuclease III / KOW domain-containing protein / Ribosomal protein S12 / Translational machinery component / Ribosomal_L6 domain-containing protein / Ribosomal protein S19/S15 / Mitochondrial ribosomal protein subunit L23 / Ribosomal protein S21 / MRP-L46 domain-containing protein / Mitochondrial 37S ribosomal protein S27 / L51_S25_CI-B8 domain-containing protein / 54S ribosomal protein L4, mitochondrial / Uncharacterized protein / 54S ribosomal protein IMG1, mitochondrial / S4 domain-containing protein / Protein FYV4, mitochondrial / PEBP-like protein / Mitochondrial ribosomal protein L37-domain-containing protein / 37S ribosomal protein mrp10, mitochondrial / Ribosomal protein L13 / 54S ribosomal protein L27, mitochondrial / RNase III domain-containing protein / Ribosomal protein L33 / Ribosomal protein L14 / Ribosomal_S7 domain-containing protein / 30S ribosomal protein S10, mitochondrial / Mitochondrial large ribosomal subunit protein / Ribosomal protein L17 / 37S ribosomal protein S9, mitochondrial / 37S ribosomal protein S8, mitochondrial / 54S ribosomal protein L31, mitochondrial / Ribosomal protein S5 / Related to ribosomal protein YmL11, mitochondrial / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL53 / Small ribosomal subunit protein uS13m / Large ribosomal subunit protein mL61 / Small ribosomal subunit protein mS27 / Large ribosomal subunit protein bL36m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein mL50 / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein mS45 / Small ribosomal subunit protein mS38 / Small ribosomal subunit protein mS26 / Related to ribosomal protein L1 / Small ribosomal subunit protein bS18m / Large ribosomal subunit protein uL3m / Small ribosomal subunit protein mS23 / Related to ribosomal protein YmL20, mitochondrial / Small ribosomal subunit protein uS5m / Related to ribosomal protein S15 (Mitochondrial) / Related to ribosomal protein L16, mitochondrial / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein uL5m / Related to ribosomal protein L34, mitochondrial / 3-hydroxyisobutyryl-CoA hydrolase / Related to ribosomal protein YmL36, mitochondrial / Small ribosomal subunit protein mS41 / Large ribosomal subunit protein bL32m / Small ribosomal subunit protein mS35 / Small ribosomal subunit protein uS2m / Large ribosomal subunit protein uL4m
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsAmunts, A. / Itoh, Y. / Naschberger, A.
Funding support Sweden, European Union, 4items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research Council (ERC)(ERC-2018-StG-805230European Union
Knut and Alice Wallenberg Foundation2018.0080 Sweden
European Molecular Biology Organization (EMBO)H2020-MSCA-IF-2017European Union
CitationJournal: Nat Commun / Year: 2020
Title: Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.
Authors: Yuzuru Itoh / Andreas Naschberger / Narges Mortezaei / Johannes M Herrmann / Alexey Amunts /
Abstract: Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each ...Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each other is not understood. We report models of the translating fungal mitoribosome with mRNA, tRNA and nascent polypeptide, as well as an assembly intermediate. Nicotinamide adenine dinucleotide (NAD) is found in the central protuberance of the large subunit, and the ATPase inhibitory factor 1 (IF) in the small subunit. The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. An assembly intermediate is modeled with the maturation factor Atp25, providing insight into the biogenesis of the mitoribosomal large subunit and translation regulation.
History
DepositionApr 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: 23S rRNA
B: 60S ribosomal protein L2, mitochondrial
C: Related to ribosomal protein L3, mitochondrial
D: 60S ribosomal protein L4, variant
E: Related to ribosomal protein L5, mitochondrial
F: uL6m
G: RIBOSOMAL_L9 domain-containing protein
f: Related to ribosomal protein YmL11, mitochondrial
g: uL11m
H: uL13m
I: Ribosomal protein L14
J: Ribosomal protein L15
K: Related to ribosomal protein L16, mitochondrial
L: uL17m
M: bL19m
N: Related to ribosomal protein YmL49, mitochondrial
O: Mitochondrial large ribosomal subunit
P: uL23m
Q: KOW domain-containing protein
R: Related to 60s ribosomal protein L2 (Mitochondrial)
S: bL28m
T: 54S ribosomal protein L4, mitochondrial
U: Related to ribosomal protein L30
V: Related to ribosomal protein YmL36, mitochondrial
W: Related to ribosomal protein YmL32 (Mitochondrial)
X: bL33m
Y: Related to ribosomal protein L34, mitochondrial
0: Ribosomal protein
1: PEBP-like protein
2: mL40
3: mL41
4: L51_S25_CI-B8 domain-containing protein
5: Ribonuclease III
6: mL46
7: mL49
8: mL50
h: Probable ribosomal protein YmL44, mitochondrial
i: mL54
9: RNase III domain-containing protein
a: Related to ribosomal protein YmL20, mitochondrial
b: Mitoc_mL59 domain-containing protein
c: 54S ribosomal protein L31, mitochondrial
d: mL67
AA: bS1m
BB: Mito ribosomal protein S2
CC: Ribosomal protein S5
DD: S4 RNA-binding domain-containing protein
EE: Related to ribosomal protein S5 (Mitochondrial)
FF: Ribosomal protein S6
GG: Ribosomal_S7 domain-containing protein
HH: uS8m
II: uS9m
JJ: 30S ribosomal protein S10, mitochondrial
KK: Translational machinery component
LL: Ribosomal protein S12
MM: Probable ribosomal protein S13
NN: Mitochondrial 37S ribosomal protein MRP2
OO: Related to ribosomal protein S15 (Mitochondrial)
PP: bS16m
QQ: uS17m
RR: Ribosomal protein S18
SS: Ribosomal protein S19/S15
TT: bS21m
UU: 37S ribosomal protein S25, mitochondrial
VV: mS26
WW: mS27
XX: Mitochondrial ribosomal protein DAP3
YY: mS33
ZZ: 37S ribosomal protein S24, mitochondrial
11: 37S ribosomal protein mrp10, mitochondrial
22: DUF1713 domain-containing protein
33: Protein FYV4, mitochondrial
44: Manganese and iron superoxide dismutase
55: Manganese and iron superoxide dismutase
66: mS45
77: mS46
88: 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
00: IF1
99: IF1
aa: 16S rRNA
bb: P-site-tRNA
ee: mRNA
cc: Poly-Peptide
e: 60S ribosomal protein L1, mitochondrial
j: L51_S25_CI-B8 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,131,734389
Polymers4,122,23885
Non-polymers9,496304
Water00
1


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

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Components

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RNA chain , 4 types, 4 molecules Aaabbee

#1: RNA chain 23S rRNA


Mass: 1114857.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus)
#78: RNA chain 16S rRNA


Mass: 600339.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus)
#79: RNA chain P-site-tRNA


Mass: 23481.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus)
#80: RNA chain mRNA


Mass: 3431.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus)

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60S ribosomal protein ... , 3 types, 3 molecules BDe

#2: Protein 60S ribosomal protein L2, mitochondrial


Mass: 42260.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DJN7
#4: Protein 60S ribosomal protein L4, variant


Mass: 36402.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: V5IMN1
#82: Protein 60S ribosomal protein L1, mitochondrial / Related to ribosomal protein L1


Mass: 33327.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q870V5

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Related to ribosomal protein ... , 12 types, 12 molecules CEfKNUVWYaEEOO

#3: Protein Related to ribosomal protein L3, mitochondrial / Translation protein


Mass: 41262.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q873B3
#5: Protein Related to ribosomal protein L5, mitochondrial / Ribosomal protein L5


Mass: 39170.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q96U12
#8: Protein Related to ribosomal protein YmL11, mitochondrial


Mass: 37363.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q6M9C4
#13: Protein Related to ribosomal protein L16, mitochondrial / Ribosomal protein L16


Mass: 27443.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q8X081
#16: Protein Related to ribosomal protein YmL49, mitochondrial


Mass: 23953.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q6MVF2
#23: Protein Related to ribosomal protein L30


Mass: 18196.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q8X098
#24: Protein Related to ribosomal protein YmL36, mitochondrial


Mass: 23766.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q9C2E5
#25: Protein Related to ribosomal protein YmL32 (Mitochondrial)


Mass: 14114.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q9HFL0
#27: Protein Related to ribosomal protein L34, mitochondrial


Mass: 14853.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q96U95
#40: Protein Related to ribosomal protein YmL20, mitochondrial


Mass: 25439.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q8NIR6
#48: Protein Related to ribosomal protein S5 (Mitochondrial)


Mass: 53297.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q8X048
#58: Protein Related to ribosomal protein S15 (Mitochondrial)


Mass: 35803.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q8X067

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Protein , 44 types, 46 molecules FGgHLMPQRSX01235678i9bdAABBDDGGHHIIJJ...

#6: Protein uL6m


Mass: 28629.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DQR9
#7: Protein RIBOSOMAL_L9 domain-containing protein


Mass: 33173.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DK80
#9: Protein uL11m


Mass: 16629.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DNH1
#10: Protein uL13m


Mass: 20334.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0E388
#14: Protein uL17m


Mass: 22181.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0ECK1
#15: Protein bL19m


Mass: 28235.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DXI2
#18: Protein uL23m


Mass: 26005.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DT83
#19: Protein KOW domain-containing protein


Mass: 45460.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DQ90
#20: Protein Related to 60s ribosomal protein L2 (Mitochondrial)


Mass: 49549.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q8X0Q2
#21: Protein bL28m


Mass: 31501.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DNQ5
#26: Protein bL33m


Mass: 7027.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0E6P7
#28: Protein Ribosomal protein


Mass: 13960.405 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S4E7
#29: Protein PEBP-like protein


Mass: 50749.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DZ96
#30: Protein mL40


Mass: 41496.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DWX0
#31: Protein mL41


Mass: 11796.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0E3D2
#33: Protein Ribonuclease III


Mass: 48106.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DPP2
#34: Protein mL46


Mass: 41322.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DTN8
#35: Protein mL49


Mass: 18180.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S518
#36: Protein mL50


Mass: 49748.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S711
#38: Protein mL54


Mass: 23179.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0E0Q5
#39: Protein RNase III domain-containing protein


Mass: 29625.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0E462
#41: Protein Mitoc_mL59 domain-containing protein


Mass: 18745.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DMU6
#43: Protein mL67


Mass: 32516.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0ECJ7
#44: Protein bS1m


Mass: 51596.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DJR9
#45: Protein Mito ribosomal protein S2


Mass: 47197.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: V5ILE0
#47: Protein S4 RNA-binding domain-containing protein


Mass: 51610.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DXP8
#50: Protein Ribosomal_S7 domain-containing protein


Mass: 33821.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0E7P2
#51: Protein uS8m


Mass: 17743.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0EEW5
#52: Protein uS9m


Mass: 35319.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0ED13
#53: Protein 30S ribosomal protein S10, mitochondrial


Mass: 30377.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0EAU9
#54: Protein Translational machinery component


Mass: 42159.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DQD8
#59: Protein bS16m


Mass: 12140.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DKS9
#60: Protein uS17m


Mass: 18505.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DJ04
#63: Protein bS21m


Mass: 25679.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DTH5
#65: Protein mS26


Mass: 35312.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SHR9
#66: Protein mS27


Mass: 44923.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RYW7
#68: Protein mS33


Mass: 12169.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DU00
#71: Protein DUF1713 domain-containing protein


Mass: 38126.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SHR6
#72: Protein Protein FYV4, mitochondrial


Mass: 26612.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q9HE52
#73: Protein Manganese and iron superoxide dismutase


Mass: 34270.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DM95
#74: Protein mS45


Mass: 39274.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SHB2
#75: Protein mS46


Mass: 43112.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DYB0
#76: Protein 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial / 3-hydroxyisobutyryl-coenzyme A hydrolase


Mass: 56401.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus)
References: UniProt: Q9C251, 3-hydroxyisobutyryl-CoA hydrolase
#77: Protein IF1


Mass: 10664.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DIK4

+
Ribosomal protein ... , 7 types, 7 molecules IJCCFFLLRRSS

#11: Protein Ribosomal protein L14


Mass: 14135.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0E7L9
#12: Protein Ribosomal protein L15


Mass: 33951.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DM93
#46: Protein Ribosomal protein S5


Mass: 58907.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A1W5YJW8
#49: Protein Ribosomal protein S6


Mass: 13304.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DP65
#55: Protein Ribosomal protein S12


Mass: 18657.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DQD0
#61: Protein Ribosomal protein S18


Mass: 28468.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q872A7
#62: Protein Ribosomal protein S19/S15


Mass: 10408.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DRW6

+
Mitochondrial ... , 3 types, 3 molecules ONNXX

#17: Protein Mitochondrial large ribosomal subunit


Mass: 41565.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7S5N0
#57: Protein Mitochondrial 37S ribosomal protein MRP2


Mass: 13210.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DHJ1
#67: Protein Mitochondrial ribosomal protein DAP3


Mass: 51451.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7SD06

+
54S ribosomal protein ... , 2 types, 2 molecules Tc

#22: Protein 54S ribosomal protein L4, mitochondrial


Mass: 29645.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DW15
#42: Protein 54S ribosomal protein L31, mitochondrial


Mass: 13131.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0EF55

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L51 S25 CI-B8 domain-containing ... , 2 types, 2 molecules 4j

#32: Protein L51_S25_CI-B8 domain-containing protein


Mass: 15126.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0DUU4
#83: Protein L51_S25_CI-B8 domain-containing protein


Mass: 22734.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q7RWZ7

+
Probable ribosomal protein ... , 2 types, 2 molecules hMM

#37: Protein Probable ribosomal protein YmL44, mitochondrial


Mass: 11128.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q6MVH6
#56: Protein Probable ribosomal protein S13 / Putative ribosomal protein S13


Mass: 13503.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q6MVY0

+
37S ribosomal protein ... , 3 types, 3 molecules UUZZ11

#64: Protein 37S ribosomal protein S25, mitochondrial


Mass: 29553.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q873E4
#69: Protein 37S ribosomal protein S24, mitochondrial


Mass: 44057.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q9P5J2
#70: Protein 37S ribosomal protein mrp10, mitochondrial


Mass: 9907.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0E339

+
Protein/peptide , 1 types, 1 molecules cc

#81: Protein/peptide Poly-Peptide


Mass: 515.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus)

+
Non-polymers , 6 types, 304 molecules

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


Mass: 24.305 Da / Num. of mol.: 250 / Source method: obtained synthetically / Formula: Mg
#85: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#86: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: K
#87: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#88: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#89: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

+
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mitoribosome of Neurospora crassa in the tRNA bound state (P-site).
Type: RIBOSOME / Entity ID: #1-#83 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Neurospora crassa (fungus) / Strain: K5-15-23-1
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid-KOHHEPES-KOH1
215 mMPotassium chlorideKCl1
315 mMMagnesium acetateMg(C2H3O2)21
40.05 %n-Dodecyl B-D-maltosideDDM1
50.0075 %1,3-bis(sn-3-phosphatidyl)-sn-glycerolCardiolipin1
62 mMDithiothreitolDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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 / Calibrated magnification: 130000 X / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3172
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20 / Used frames/image: 1-20

-
Processing

Software
NameVersionClassification
phenix.real_space_refinedev_3714refinement
PHENIXdev_3714refinement
EM software
IDNameCategory
2EPUimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24601 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 21.41 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026231578
ELECTRON MICROSCOPYf_angle_d0.3854334011
ELECTRON MICROSCOPYf_chiral_restr0.030940372
ELECTRON MICROSCOPYf_plane_restr0.001926583
ELECTRON MICROSCOPYf_dihedral_angle_d20.2441101729

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