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- PDB-6yws: The structure of the large subunit of the mitoribosome from Neuro... -

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Basic information

Entry
Database: PDB / ID: 6yws
TitleThe structure of the large subunit of the mitoribosome from Neurospora crassa
Components
  • (50S ribosomal protein ...) x 5
  • (54S ribosomal protein ...) x 2
  • (60S ribosomal protein ...) x 9
  • (Mitochondrial large ribosomal ...) x 2
  • (Mitochondrial ribosomal protein ...) x 4
  • (Ribosomal protein ...) x 2
  • (Uncharacterized ...) x 10
  • 50S ribosomal subunit L30
  • Aconitate hydrataseAconitase
  • KOW domain-containing protein
  • L51_S25_CI-B8 domain-containing protein
  • Mitoc_mL59 domain-containing protein
  • Mitochondrial ribosomal protein
  • RIBOSOMAL_L9 domain-containing protein
  • RNA (2820-MER)
  • RNase III domain-containing protein
  • Related to ribosomal protein L34, mitochondrial
  • Ribosomal protein
KeywordsTRANSLATION / Neurospora crassa / translating Mitoribosomes / tRNA / mRNA / mL108
Function / homology
Function and homology information


DNA strand exchange activity / mitochondrial genome maintenance / ribonuclease III activity / fungal-type vacuole / mitochondrial large ribosomal subunit / mitochondrial translation / RNA processing / large ribosomal subunit rRNA binding / large ribosomal subunit / single-stranded DNA binding ...DNA strand exchange activity / mitochondrial genome maintenance / ribonuclease III activity / fungal-type vacuole / mitochondrial large ribosomal subunit / mitochondrial translation / RNA processing / large ribosomal subunit rRNA binding / large ribosomal subunit / single-stranded DNA binding / double-stranded RNA binding / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding
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 / Ribonuclease-III-like / 28S ribosomal protein S25, mitochondrial / Ribonuclease III family domain profile. / Ribosomal protein L37, mitochondrial / Mitochondrial ribosomal protein L37 / Ribonuclease III family / Ribonuclease III domain / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / 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 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double-stranded RNA-binding domain / : / Ribosomal protein/NADH dehydrogenase domain / NUDIX domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NUDIX hydrolase domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / NUDIX hydrolase-like domain superfamily / Ribosomal protein L10-like domain superfamily / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal protein L28/L24 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 L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L14P, bacterial-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 L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal protein L17
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L15 / Large ribosomal subunit protein mL59 domain-containing protein / Uncharacterized protein ...: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L15 / Large ribosomal subunit protein mL59 domain-containing protein / Uncharacterized protein / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein bL32m / 60S ribosomal protein L1 / Large ribosomal subunit protein uL5m / Large ribosomal subunit protein mL58 / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein bL31m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL3m / 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 / Large ribosomal subunit protein mL67 / 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 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein bL36m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein mL44 / 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 / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL53 / Related to ribosomal protein L34, mitochondrial / Large ribosomal subunit protein mL60 / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL4m
Similarity search - Component
Biological speciesNeurospora crassa OR74A (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 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: RNA (2820-MER)
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: Uncharacterized protein
g: 60S ribosomal protein L19
H: Ribosomal protein L13
I: 50S ribosomal protein L14
J: Ribosomal 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: Uncharacterized protein
S: 50S ribosomal protein L24
T: 54S ribosomal protein L4, mitochondrial
U: 50S ribosomal protein L30
V: Uncharacterized protein
W: Mitochondrial ribosomal protein subunit L32
X: Uncharacterized protein
Y: Related to ribosomal protein L34, mitochondrial
0: Ribosomal protein
1: Mitochondrial large ribosomal subunit YmL35
2: Uncharacterized protein
3: Uncharacterized protein
4: Mitochondrial ribosomal protein L43
5: 60S ribosomal protein L3
6: 50S ribosomal subunit L30
7: Uncharacterized protein
8: Uncharacterized protein
h: Mitochondrial ribosomal protein L44
i: Uncharacterized protein
9: RNase III domain-containing protein
a: 60S ribosomal protein L20
b: Mitoc_mL59 domain-containing protein
c: 54S ribosomal protein L31, mitochondrial
d: Uncharacterized protein
e: 60S ribosomal protein L1
j: L51_S25_CI-B8 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,367,412224
Polymers2,361,98545
Non-polymers5,427179
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 , 1 types, 1 molecules A

#1: RNA chain RNA (2820-MER)


Mass: 1114857.375 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
#44: 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 , 10 types, 10 molecules GMNQY069bj

#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
#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
#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
#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: Q96U95
#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
#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
#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
#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 OR74A (fungus) / References: UniProt: A0A0B0DMU6
#45: 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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Uncharacterized ... , 10 types, 10 molecules fRVX2378id

#8: Protein Uncharacterized protein


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


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 Uncharacterized protein


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 Uncharacterized protein


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


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 Uncharacterized protein


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 Uncharacterized protein


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 Uncharacterized protein


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 Uncharacterized protein


Mass: 23179.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa OR74A (fungus) / References: UniProt: Q7SCZ3
#43: Protein Uncharacterized protein


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

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Ribosomal protein ... , 2 types, 2 molecules HJ

#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
#12: Protein Ribosomal 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: A0A0B0DM93

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Mitochondrial large ribosomal ... , 2 types, 2 molecules O1

#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
#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

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Mitochondrial ribosomal protein ... , 4 types, 4 molecules PW4h

#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
#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

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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

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Non-polymers , 5 types, 179 molecules

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


Mass: 24.305 Da / Num. of mol.: 163 / Source method: obtained synthetically / Formula: Mg
#47: Chemical ChemComp-SPM / SPERMINE / Spermine


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


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#49: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#50: 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

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Details

Has ligand of interestY

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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: Mitoribosome of Neurospora crassa / Type: RIBOSOME / Entity ID: #1-#45 / 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_3742refinement
PHENIXdev_3742refinement
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: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131806 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 41.16 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0018134314
ELECTRON MICROSCOPYf_angle_d0.3742195115
ELECTRON MICROSCOPYf_chiral_restr0.0323826
ELECTRON MICROSCOPYf_plane_restr0.002314493
ELECTRON MICROSCOPYf_dihedral_angle_d19.738559946

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Jul 12, 2017. Major update of PDB

Major update of PDB

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

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

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Yorodumi

Thousand views of thousand structures

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

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

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