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- PDB-6ywx: The structure of the mitoribosome from Neurospora crassa with tRN... -

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Basic information

Entry
Database: PDB / ID: 6ywx
TitleThe structure of the mitoribosome from Neurospora crassa with tRNA bound to the E-site
Components
  • (37S ribosomal protein ...) x 6
  • (40S ribosomal protein ...) x 2
  • (50S ribosomal protein ...) x 5
  • (50S ribosomal subunit ...) x 2
  • (54S ribosomal protein ...) x 2
  • (60S ribosomal protein ...) x 9
  • (Mito ribosomal protein ...) x 5
  • (Mitochondrial ...Mitochondrion) x 14
  • (Ribosomal protein ...) x 4
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
  • Aconitate hydrataseAconitase
  • DUF1713 domain-containing protein
  • Fe superoxide dismutase
  • IF1
  • IGR domain-containing protein
  • KOW domain-containing protein
  • L51_S25_CI-B8 domain-containing protein
  • RIBOSOMAL_L9 domain-containing protein
  • RNase III domain-containing protein
  • Related to ribosomal protein L34, mitochondrial
  • Ribosomal protein
  • Ribosomal_S7 domain-containing protein
  • bL27m
  • bL31m
  • bL33m
  • bS1m
  • mL40
  • mL41
  • mL49
  • mL50
  • mL54
  • mL67
  • mS26
  • mS27
  • mS33
  • mS45
  • mS46
  • tRNA E-site
  • uL10m
KeywordsTRANSLATION / Neurospora crassa / translating Mitoribosomes / tRNA / mRNA / mL108
Function / homology
Function and homology information


3-hydroxyisobutyryl-CoA hydrolase activity / nuclear pore inner ring / valine catabolic process / nuclear pore organization / DNA strand exchange activity / ATPase inhibitor activity / mitochondrial genome maintenance / ribonuclease III activity / fungal-type vacuole / negative regulation of ATP-dependent activity ...3-hydroxyisobutyryl-CoA hydrolase activity / nuclear pore inner ring / valine catabolic process / nuclear pore organization / DNA strand exchange activity / ATPase inhibitor activity / mitochondrial genome maintenance / ribonuclease III activity / fungal-type vacuole / negative regulation of ATP-dependent activity / mitochondrial large ribosomal subunit / structural constituent of nuclear pore / positive regulation of translational fidelity / mitochondrial small ribosomal subunit / mitochondrial translation / superoxide dismutase activity / RNA processing / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / double-stranded RNA binding / large ribosomal subunit / single-stranded DNA binding / small ribosomal subunit / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / mitochondrion / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
54S ribosomal protein L44, mitochondrial / : / Mitochondrial ribosomal protein subunit L20 / Ribosomal protein L31p, N-terminal / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L25 / 54S ribosomal protein L15, mitochondrial / MRPL25 domain / 54S ribosomal protein L3, double-stranded RNA binding domain ...54S ribosomal protein L44, mitochondrial / : / Mitochondrial ribosomal protein subunit L20 / Ribosomal protein L31p, N-terminal / Ribosomal protein L20, mitochondrial / Mitochondrial homologous recombination protein 1 / 54S ribosomal protein L25 / 54S ribosomal protein L15, mitochondrial / MRPL25 domain / 54S ribosomal protein L3, double-stranded RNA binding domain / Transcriptional regulation of mitochondrial recombination / Mitochondrial ribosomal protein mL59 / 54S ribosomal protein L28, mitochondrial / Ribosomal protein L31, mitochondrial / 54S ribosomal protein L36, yeast / Mitochondrial ribosomal protein L31 / 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 MRP10, mitochondrial / Ribosomal protein S35, mitochondrial / Eukaryotic mitochondrial regulator protein / Enoyl-CoA hydratase/isomerase domain / IGR protein motif / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / Ribonuclease-III-like / IGR protein motif / IGR / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / 28S ribosomal protein S25, mitochondrial / Ribonuclease III family domain profile. / Ribosomal protein L37, mitochondrial / Mitochondrial ribosomal protein L37 / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Ribonuclease III family / Ribonuclease III domain / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Ribosomal protein L49/IMG2 / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial large subunit ribosomal protein (Img2) / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Enoyl-CoA hydratase/isomerase, conserved site / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Enoyl-CoA hydratase/isomerase signature. / Ribosomal protein L50, mitochondria / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal subunit 39S / 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 / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double-stranded RNA-binding domain / : / NUDIX domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NUDIX hydrolase domain / ClpP/crotonase-like domain superfamily / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / NUDIX hydrolase-like domain superfamily / Ribosomal protein L11, bacterial-type / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Sterile alpha motif/pointed domain superfamily / Ribosomal protein S21 / Ribosomal protein L10-like domain superfamily / :
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein ...ADENOSINE-5'-TRIPHOSPHATE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / 37S ribosomal protein mrp5 / Large ribosomal subunit protein uL16m / Ribosomal protein S16, mitochondrial / Ribosomal protein S5, mitochondrial / Large ribosomal subunit protein bL32m / 37S ribosomal protein S5 / Ribosomal protein S15 / Mitochondrial 37S ribosomal protein S27 / 37S ribosomal protein S24, mitochondrial / 60S ribosomal protein L1 / Large ribosomal subunit protein uL5m / Protein FYV4, mitochondrial / Large ribosomal subunit protein mL58 / Large ribosomal subunit protein bL27m / Mitochondrial 3-hydroxyisobutyryl-CoA hydrolase / Large ribosomal subunit protein bL31m / Ribosomal protein L34 / Large ribosomal subunit protein bL17m / Mito ribosomal protein S18 / Large ribosomal subunit protein uL3m / Mitochondrial ribosomal protein S19 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein mL61 / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein mL38 / 37S ribosomal protein S10, mitochondrial / Large ribosomal subunit protein mL67 / Small ribosomal subunit protein mS27 / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein uL6m / RIBOSOMAL_L9 domain-containing protein / Large ribosomal subunit protein mL57 / Large ribosomal subunit protein mL46 / 40S ribosomal protein S13 / Fe superoxide dismutase / Large ribosomal subunit protein mL43 / Mitochondrial 37S ribosomal protein S17 / Large ribosomal subunit protein bL36m / 37S ribosomal protein mrp10, mitochondrial / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein mL41 / Ribosomal_S7 domain-containing protein / Large ribosomal subunit protein mL50 / 37S ribosomal protein S9, mitochondrial / Large ribosomal subunit protein uL29m / Mitochondrial 30S ribosomal protein S12 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein mL44 / Mito ribosomal protein S4 / Mito ribosomal protein S21 / Mito ribosomal protein S6 / 50S ribosomal subunit protein L15 / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein uL13m / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein mL54 / Small ribosomal subunit protein mS29 / Mitochondrial 60S ribosomal protein L25 / Mitochondrial 40S ribosomal protein MRP2 / Protein FYV4, mitochondrial / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL53 / Mitochondrial ribosomal protein subunit S18 / Small ribosomal subunit protein mS45 / 40S ribosomal protein S8 / Small ribosomal subunit protein mS38 / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein mS23 / Large ribosomal subunit protein mL60 / Small ribosomal subunit protein uS2m / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL4m / ATP synthase F1 subunit epsilon
Similarity search - Component
Biological speciesNeurospora crassa OR74A (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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

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Structure visualization

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Assembly

Deposited unit
A: 23S rRNA
B: 60S ribosomal protein L2
C: 60S ribosomal protein L3
D: 60S ribosomal protein L4, variant
E: 50S ribosomal protein L5
F: 60S ribosomal protein L6
G: RIBOSOMAL_L9 domain-containing protein
f: uL10m
g: 60S ribosomal protein L19
H: Ribosomal protein L13
I: 50S ribosomal protein L14
J: 50S ribosomal subunit protein L15
K: 60S ribosomal protein L16
L: 50S ribosomal protein L17
M: Mitochondrial ribosomal protein
N: Aconitate hydratase
O: Mitochondrial large ribosomal subunit
P: Mitochondrial ribosomal protein subunit L23
Q: KOW domain-containing protein
R: bL27m
S: 50S ribosomal protein L24
T: 54S ribosomal protein L4, mitochondrial
U: 50S ribosomal protein L30
V: bL31m
W: Mitochondrial ribosomal protein subunit L32
X: bL33m
Y: Related to ribosomal protein L34, mitochondrial
0: Ribosomal protein
1: Mitochondrial large ribosomal subunit YmL35
2: mL40
3: mL41
4: Mitochondrial ribosomal protein L43
5: 60S ribosomal protein L3
6: 50S ribosomal subunit L30
7: mL49
8: mL50
h: Mitochondrial ribosomal protein L44
i: mL54
9: RNase III domain-containing protein
a: 60S ribosomal protein L20
b: Mitochondrial 60S ribosomal protein L25
c: 54S ribosomal protein L31, mitochondrial
d: mL67
AA: bS1m
BB: Mito ribosomal protein S2
CC: Ribosomal protein S5, mitochondrial
DD: Mito ribosomal protein S4
EE: 37S ribosomal protein S5
FF: Mito ribosomal protein S6
GG: Ribosomal_S7 domain-containing protein
HH: 40S ribosomal protein S8
II: 37S ribosomal protein S9, mitochondrial
JJ: 37S ribosomal protein S10, mitochondrial
KK: Mitochondrial ribosomal protein subunit S18
LL: Mitochondrial 30S ribosomal protein S12
MM: 40S ribosomal protein S13
NN: Mitochondrial 40S ribosomal protein MRP2
OO: Ribosomal protein S15
PP: Ribosomal protein S16, mitochondrial
QQ: Mitochondrial 37S ribosomal protein S17
RR: Mito ribosomal protein S18
SS: Mitochondrial ribosomal protein S19
TT: Mito ribosomal protein S21
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: IGR domain-containing protein
44: Fe superoxide dismutase
55: Fe superoxide dismutase
66: mS45
77: mS46
88: 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial
00: IF1
99: IF1
aa: 16S rRNA
bb: tRNA E-site
e: 60S ribosomal protein L1
j: L51_S25_CI-B8 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,123,915387
Polymers4,114,40483
Non-polymers9,511304
Water0
1


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

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Components

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RNA chain , 3 types, 3 molecules Aaabb

#1: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 1114857.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (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 OR74A (fungus) / References: GenBank: 452883339
#79: RNA chain tRNA E-site


Mass: 19593.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus)

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60S ribosomal protein ... , 9 types, 9 molecules BCDFgK5ae

#2: Protein 60S ribosomal protein L2 /


Mass: 42260.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SCX7
#3: Protein 60S ribosomal protein L3 /


Mass: 41262.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8T6
#4: Protein 60S ribosomal protein L4, variant / Ribosome


Mass: 36402.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: V5IMN1
#6: Protein 60S ribosomal protein L6 /


Mass: 28629.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RZF0
#9: Protein 60S ribosomal protein L19 /


Mass: 16629.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RX40
#13: Protein 60S ribosomal protein L16 /


Mass: 27443.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: F5HIJ5
#33: Protein 60S ribosomal protein L3 /


Mass: 48106.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SA88
#40: Protein 60S ribosomal protein L20 /


Mass: 25439.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K6U7
#80: Protein 60S ribosomal protein L1 /


Mass: 33327.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K699

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50S ribosomal protein ... , 5 types, 5 molecules EILSU

#5: Protein 50S ribosomal protein L5 /


Mass: 39170.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K6P0
#11: Protein 50S ribosomal protein L14 /


Mass: 14135.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SBJ8
#14: Protein 50S ribosomal protein L17 /


Mass: 22181.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8C8
#21: Protein 50S ribosomal protein L24 /


Mass: 31501.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SC44
#23: Protein 50S ribosomal protein L30 /


Mass: 18196.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8Y7

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Protein , 29 types, 31 molecules GfNQRVXY02378i9dAAGGVVWWYY223344556677880099j

#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 OR74A (fungus) / References: UniProt: Q7S054
#8: Protein uL10m


Mass: 37363.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RZ62
#16: Protein Aconitate hydratase / Aconitase


Mass: 23953.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SGE5
#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 OR74A (fungus) / References: UniProt: Q7RXU7
#20: Protein bL27m


Mass: 49549.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K730
#24: Protein bL31m


Mass: 23766.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K7L7
#26: Protein bL33m


Mass: 7027.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: V5IM60
#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 OR74A (fungus) / References: UniProt: Q1K7P9
#28: Protein Ribosomal protein /


Mass: 13960.405 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S4E7
#30: Protein mL40


Mass: 41496.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (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 OR74A (fungus) / References: UniProt: Q7S5W0
#35: Protein mL49


Mass: 18180.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (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 OR74A (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 OR74A (fungus) / References: UniProt: Q7SCZ3
#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 OR74A (fungus) / References: UniProt: Q7S1R6
#43: Protein mL67


Mass: 32516.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RYM5
#44: Protein bS1m


Mass: 51596.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: A7UWX2
#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 OR74A (fungus) / References: UniProt: Q7S6M9
#65: Protein mS26


Mass: 35312.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (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 OR74A (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 OR74A (fungus) / References: UniProt: Q1K5R0
#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 OR74A (fungus) / References: UniProt: Q7SHR6
#72: Protein IGR domain-containing protein


Mass: 26612.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K6Q3
#73: Protein Fe superoxide dismutase


Mass: 34270.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S2H6
#74: Protein mS45


Mass: 39274.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (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 OR74A (fungus) / References: UniProt: Q7SG49
#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 OR74A (fungus)
References: UniProt: Q1K7A4, 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 OR74A (fungus) / References: UniProt: V5IRA3
#81: 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 OR74A (fungus) / References: UniProt: Q7RWZ7

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Ribosomal protein ... , 4 types, 4 molecules HCCOOPP

#10: Protein Ribosomal protein L13 / 60S ribosomal protein L13


Mass: 20334.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SBV6
#46: Protein Ribosomal protein S5, mitochondrial / Ribosome


Mass: 58907.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: P23351
#58: Protein Ribosomal protein S15 /


Mass: 35803.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K5G1
#59: Protein Ribosomal protein S16, mitochondrial / Ribosome / S24


Mass: 12140.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: P08580

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50S ribosomal subunit ... , 2 types, 2 molecules J6

#12: Protein 50S ribosomal subunit protein L15 /


Mass: 33951.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SB98
#34: Protein 50S ribosomal subunit L30 /


Mass: 41322.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S1Z3

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Mitochondrial ... , 14 types, 14 molecules MOPW14hbKKLLNNQQSSXX

#15: Protein Mitochondrial ribosomal protein


Mass: 28235.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RYW8
#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 OR74A (fungus) / References: UniProt: Q7S5N0
#18: Protein Mitochondrial ribosomal protein subunit L23


Mass: 26005.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SA60
#25: Protein Mitochondrial ribosomal protein subunit L32


Mass: 14114.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K4P1
#29: Protein Mitochondrial large ribosomal subunit YmL35


Mass: 50749.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RXV8
#32: Protein Mitochondrial ribosomal protein L43


Mass: 15126.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S300
#37: Protein Mitochondrial ribosomal protein L44


Mass: 11128.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SGH0
#41: Protein Mitochondrial 60S ribosomal protein L25


Mass: 18745.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SEK9
#54: Protein Mitochondrial ribosomal protein subunit S18


Mass: 42159.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SGU0
#55: Protein Mitochondrial 30S ribosomal protein S12


Mass: 18657.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S9I4
#57: Protein Mitochondrial 40S ribosomal protein MRP2


Mass: 13210.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SF85
#60: Protein Mitochondrial 37S ribosomal protein S17


Mass: 18505.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S4E0
#62: Protein Mitochondrial ribosomal protein S19


Mass: 10408.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8V2
#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 OR74A (fungus) / References: UniProt: Q7SD06

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

#22: Protein 54S ribosomal protein L4, mitochondrial / Ribosome


Mass: 29645.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S910
#42: Protein 54S ribosomal protein L31, mitochondrial / Ribosome


Mass: 13131.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: U9W8F2

+
Mito ribosomal protein ... , 5 types, 5 molecules BBDDFFRRTT

#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 OR74A (fungus) / References: UniProt: V5ILE0
#47: Protein Mito ribosomal protein S4


Mass: 51610.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SA90
#49: Protein Mito ribosomal protein S6


Mass: 13304.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SB95
#61: Protein Mito ribosomal protein S18


Mass: 28468.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K8E0
#63: Protein Mito ribosomal protein S21


Mass: 25679.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SAJ1

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37S ribosomal protein ... , 6 types, 6 molecules EEIIJJUUZZ11

#48: Protein 37S ribosomal protein S5 /


Mass: 53297.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K548
#52: Protein 37S ribosomal protein S9, mitochondrial / Ribosome / Mitochondrial ribosomal protein 9


Mass: 35319.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S7R6
#53: Protein 37S ribosomal protein S10, mitochondrial / Ribosome / Mitochondrial ribosomal small subunit protein 10


Mass: 30377.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7RYL4
#64: Protein 37S ribosomal protein S25, mitochondrial / Ribosome


Mass: 29553.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q873E4
#69: Protein 37S ribosomal protein S24, mitochondrial / Ribosome


Mass: 44057.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q1K5Z0
#70: Protein 37S ribosomal protein mrp10, mitochondrial / Ribosome


Mass: 9907.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S4Y4

+
40S ribosomal protein ... , 2 types, 2 molecules HHMM

#51: Protein 40S ribosomal protein S8 /


Mass: 17743.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SHF3
#56: Protein 40S ribosomal protein S13 /


Mass: 13503.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7S2C2

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Non-polymers , 6 types, 304 molecules

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


Mass: 24.305 Da / Num. of mol.: 249 / Source method: obtained synthetically / Formula: Mg
#83: Chemical ChemComp-SPM / SPERMINE / Spermine


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


Mass: 39.098 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: K
#85: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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
#86: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#87: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine 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

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Details

Has ligand of interestY

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Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mitoribosome of Neurospora crassa with tRNA in the E-site
Type: RIBOSOME / Entity ID: #1-#81 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Neurospora crassa OR74A (fungus)
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

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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 FIELDBright-field microscopy / 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

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23802 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 47.48 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026230536
ELECTRON MICROSCOPYf_angle_d0.4034332463
ELECTRON MICROSCOPYf_chiral_restr0.031140174
ELECTRON MICROSCOPYf_plane_restr0.00226491
ELECTRON MICROSCOPYf_dihedral_angle_d21.0453101262

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